https://wiki.anunna.wur.nl/api.php?action=feedcontributions&feedformat=atom&user=Vande018 2026-04-18T01:38:47Z User contributions MediaWiki 1.43.1 https://wiki.anunna.wur.nl/index.php?title=File:HPC_advanced_course_20211021.pdf&diff=2145 2021-11-15T09:43:29Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2144 2021-11-15T09:41:36Z

<p>Vande018: </p> <hr /> <div>== HPC Advanced Course - November 2021 ==<br /> <br /> A course for experienced users oth the Anunna HPC was organised in November 2021, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20211021.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - November 2021==<br /> <br /> Two courses for beginners was given in November 2021, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20211012.pdf|HPC Basic Course]]<br /> <br /> == Linux Basic Course - November 2021 ==<br /> <br /> A course for beginners was given in November 2021, to help beginner Linux users gain some skills in using Linux.<br /> <br /> <br /> == HPC Basic Course - 2019-11-14==<br /> <br /> A course for beginners was given on the 14th of November, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20191111.pdf|HPC Basic Course]]<br /> <br /> == HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners was given on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-06-27 ==<br /> <br /> A course for beginners was given on the 13th of June, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC CUDA/AI Course - 2019-06-21 ==<br /> <br /> A course for interested users for deep learning and neural networks, combined with some deep level manipulation of graphics cards was given by Dell on the 21st of July.<br /> <br /> [[File:WUR_CUDA_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_AI_101_210619.pdf|WUR AI Course 101]]<br /> [[File:WUR_AI_201_210619.pdf|WUR AI Course 201]]<br /> <br /> [[File:WUR_CUDA_2_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_Deep_Learning_Frameworks_210619.pdf|WUR Deep Learning Frameworks Primer]]<br /> [[File:WUR_Deep_Learning_Lab_210619.pdf|WUR Deep Learning Lab]]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_basic_course_20211012.pdf&diff=2143 2021-11-15T09:36:18Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2142 2021-11-15T09:33:36Z

<p>Vande018: </p> <hr /> <div>== HPC Basic Course - November 2021==<br /> <br /> Two courses for beginners was given in November 2021, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20211012.pdf|HPC Basic Course]]<br /> <br /> == HPC Basic Course - 2019-11-14==<br /> <br /> A course for beginners was given on the 14th of November, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20191111.pdf|HPC Basic Course]]<br /> <br /> == HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners was given on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-06-27 ==<br /> <br /> A course for beginners was given on the 13th of June, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC CUDA/AI Course - 2019-06-21 ==<br /> <br /> A course for interested users for deep learning and neural networks, combined with some deep level manipulation of graphics cards was given by Dell on the 21st of July.<br /> <br /> [[File:WUR_CUDA_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_AI_101_210619.pdf|WUR AI Course 101]]<br /> [[File:WUR_AI_201_210619.pdf|WUR AI Course 201]]<br /> <br /> [[File:WUR_CUDA_2_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_Deep_Learning_Frameworks_210619.pdf|WUR Deep Learning Frameworks Primer]]<br /> [[File:WUR_Deep_Learning_Lab_210619.pdf|WUR Deep Learning Lab]]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2065 2019-12-05T10:19:12Z

<p>Vande018: /* HPC Basic Course - 2019-11-14 */</p> <hr /> <div>== HPC Basic Course - 2019-11-14==<br /> <br /> A course for beginners was given on the 14th of November, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20191111.pdf|HPC Basic Course]]<br /> <br /> == HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners was given on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-06-27 ==<br /> <br /> A course for beginners was given on the 13th of June, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC CUDA/AI Course - 2019-06-21 ==<br /> <br /> A course for interested users for deep learning and neural networks, combined with some deep level manipulation of graphics cards was given by Dell on the 21st of July.<br /> <br /> [[File:WUR_CUDA_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_AI_101_210619.pdf|WUR AI Course 101]]<br /> [[File:WUR_AI_201_210619.pdf|WUR AI Course 201]]<br /> <br /> [[File:WUR_CUDA_2_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_Deep_Learning_Frameworks_210619.pdf|WUR Deep Learning Frameworks Primer]]<br /> [[File:WUR_Deep_Learning_Lab_210619.pdf|WUR Deep Learning Lab]]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_basic_course_20191111.pdf&diff=2064 2019-12-05T10:17:25Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2063 2019-12-05T10:16:51Z

<p>Vande018: </p> <hr /> <div>== HPC Basic Course - 2019-11-14==<br /> <br /> A course for beginners was given on the 14th of November, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20191111.pdf|HPC Basic Course]]<br /> <br /> == HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners was given on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-06-27 ==<br /> <br /> A course for beginners was given on the 13th of June, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC CUDA/AI Course - 2019-06-21 ==<br /> <br /> A course for interested users for deep learning and neural networks, combined with some deep level manipulation of graphics cards was given by Dell on the 21st of July.<br /> <br /> [[File:WUR_CUDA_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_AI_101_210619.pdf|WUR AI Course 101]]<br /> [[File:WUR_AI_201_210619.pdf|WUR AI Course 201]]<br /> <br /> [[File:WUR_CUDA_2_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_Deep_Learning_Frameworks_210619.pdf|WUR Deep Learning Frameworks Primer]]<br /> [[File:WUR_Deep_Learning_Lab_210619.pdf|WUR Deep Learning Lab]]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2062 2019-12-05T10:13:36Z

<p>Vande018: /* Upcoming Linux Basic Course - 2019-06-27 */</p> <hr /> <div>== HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners was given on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Linux Basic Course - 2019-06-27 ==<br /> <br /> A course for beginners was given on the 13th of June, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC CUDA/AI Course - 2019-06-21 ==<br /> <br /> A course for interested users for deep learning and neural networks, combined with some deep level manipulation of graphics cards was given by Dell on the 21st of July.<br /> <br /> [[File:WUR_CUDA_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_AI_101_210619.pdf|WUR AI Course 101]]<br /> [[File:WUR_AI_201_210619.pdf|WUR AI Course 201]]<br /> <br /> [[File:WUR_CUDA_2_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_Deep_Learning_Frameworks_210619.pdf|WUR Deep Learning Frameworks Primer]]<br /> [[File:WUR_Deep_Learning_Lab_210619.pdf|WUR Deep Learning Lab]]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2061 2019-12-05T10:13:10Z

<p>Vande018: /* HPC Basic Course - 2019-06-28 */</p> <hr /> <div>== HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners was given on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Upcoming Linux Basic Course - 2019-06-27 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == HPC CUDA/AI Course - 2019-06-21 ==<br /> <br /> A course for interested users for deep learning and neural networks, combined with some deep level manipulation of graphics cards was given by Dell on the 21st of July.<br /> <br /> [[File:WUR_CUDA_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_AI_101_210619.pdf|WUR AI Course 101]]<br /> [[File:WUR_AI_201_210619.pdf|WUR AI Course 201]]<br /> <br /> [[File:WUR_CUDA_2_210619.pdf|WUR CUDA Course]]<br /> [[File:WUR_Deep_Learning_Frameworks_210619.pdf|WUR Deep Learning Frameworks Primer]]<br /> [[File:WUR_Deep_Learning_Lab_210619.pdf|WUR Deep Learning Lab]]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2025 2019-06-04T14:42:41Z

<p>Vande018: /* Upcoming Linux Basic Course - 2019-06-13 */</p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_advanced_slides_20190528.pdf&diff=2024 2019-06-04T14:41:54Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_advanced_course_20190506.pdf&diff=2023 2019-06-04T14:41:30Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2022 2019-06-04T14:40:48Z

<p>Vande018: /* HPC Advanced Course - 2019-05-28 */</p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> [[File:Example.jpg]]== HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2021 2019-06-04T14:39:14Z

<p>Vande018: /* HPC Advanced Course - 2019-05-28 */</p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_advanced_course_20190506.pdf|Advanced Course 1]]<br /> [[File:HPC_advanced_slides_20190528.pdf|Advanced Course 2]]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2020 2019-06-04T14:07:34Z

<p>Vande018: /* Upcoming: HPC Advanced Course - 2019-05-28 */</p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users was organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2018 2019-05-09T08:50:30Z

<p>Vande018: /* HPC Basic Course - 2019-05-07 */</p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == Upcoming: HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users will be organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> You can register [http://https://www.wur.nl/nl/activiteit/High-Performance-Computing-Cluster-advanced-course-on-28-May-2019.htm here]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC basic course 20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_basic_course_20190506.pdf&diff=2017 2019-05-09T08:45:49Z

<p>Vande018: Vande018 uploaded a new version of File:HPC basic course 20190506.pdf</p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_basic_course_20190506.pdf&diff=2016 2019-05-09T08:45:15Z

<p>Vande018: Vande018 uploaded a new version of File:HPC basic course 20190506.pdf</p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_basic_course_20190506.pdf&diff=2015 2019-05-09T08:43:47Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=2014 2019-05-09T08:42:59Z

<p>Vande018: /* HPC Basic Course - 2019-05-07 */</p> <hr /> <div>== Upcoming: HPC Basic Course - 2019-06-28==<br /> <br /> A course for beginners will be organised on the 28th of June, aiming to help absolute beginners to begin to use the main job scheduler, SLURM. You can register [https://oneschool.wur.nl/Lists/Cursus/DispForm.aspx?ID=100 here].<br /> <br /> == Upcoming Linux Basic Course - 2019-06-13 ==<br /> <br /> A course for beginners will be organised on the 13th of June, to help beginner Linux users gain some skills in using Linux. You can register for this course [https://www.wur.nl/en/activity/Linux-basic-course-on-13-June-2019.htm here]<br /> <br /> == Upcoming: HPC Advanced Course - 2019-05-28 ==<br /> <br /> A course for experienced users will be organised on the 28th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> You can register [http://https://www.wur.nl/nl/activiteit/High-Performance-Computing-Cluster-advanced-course-on-28-May-2019.htm here]<br /> <br /> == HPC Basic Course - 2019-05-07 ==<br /> <br /> A course for beginners will be organised on the 7th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20190506.pdf|Basic Course]]<br /> <br /> == Linux Basic Course - 2019-04-16 ==<br /> <br /> A course for beginners was organised on the 16th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=1913 2018-10-17T06:39:51Z

<p>Vande018: /* Basic Linux Course - 2018-10-02 */</p> <hr /> <div>== HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=1912 2018-10-17T06:38:53Z

<p>Vande018: /* Basic Linux Course - 2018-10-02 */</p> <hr /> <div>== HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> [https://etherpad.lug.wur.nl/p/UpkF2KXDVh|Summary]<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_advanced_course_20181008.pdf&diff=1911 2018-10-16T12:04:37Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=1910 2018-10-16T12:04:15Z

<p>Vande018: </p> <hr /> <div>== HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=File:HPC_basic_course_20181008.pdf&diff=1909 2018-10-16T12:02:38Z

<p>Vande018: </p> <hr /> <div></div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=1908 2018-10-16T12:02:10Z

<p>Vande018: /* HPC Basic Course - 2018-10-11 */</p> <hr /> <div>== HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> [[File:HPC_basic_course_20181008.pdf|Basic Course]]<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Courses&diff=1907 2018-10-16T11:59:36Z

<p>Vande018: </p> <hr /> <div>== HPC Advanced Course - 2018-10-16 ==<br /> <br /> A course for experienced users was organised on the 16th of October, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_Slides_20181016.pdf|Advanced Course (Gwen)]]<br /> [[File:HPC_advanced_course_20181008.pdf|Advanced Course (Jeremie)]]<br /> <br /> == HPC Basic Course - 2018-10-11 ==<br /> <br /> A course for beginners was organised on the 11th of October, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-10-02 ==<br /> <br /> A course basic Linux usage was organised on the 2nd of October, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2018-05-18 ==<br /> <br /> A course for experienced users was organised on the 18th of May, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_20180518-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> == HPC Basic Course - 2018-05-17 ==<br /> <br /> A course for beginners was organised on the 17th of May, aiming to help absolute beginners to begin to use the main job scheduler, SLURM.<br /> <br /> == Basic Linux Course - 2018-04-19 ==<br /> <br /> A course basic Linux usage was organised on the 19th of April, to help beginner Linux users gain some skills in using Linux.<br /> <br /> == HPC Advanced Course - 2017-11-09 ==<br /> <br /> A course for experienced users was organised on the 9th of November, aiming to brush up users on techniques for submitting unusual jobs, and help provide some more helpful hints and techniques.<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-JV.pdf|Advanced Course (Jeremie)]]<br /> <br /> [[File:HPC_Advanced_course_2017-11-08-GD.pdf|Advanced Course (Gwen)]]<br /> <br /> [[File:Checkpointing_2017-11-08.pdf|Checkpointing]]<br /> <br /> == HPC Basic Course - 2017-10-30 ==<br /> <br /> A course for beginners was organised on the 30th of October, aiming to help absolute beginners to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:HPC_basic_course_20171025.pdf | Basic introduction to Linux]]<br /> <br /> == HPC Teaching - 2017-06-07 ==<br /> <br /> A course for was organised on the 7th of June, aiming to help absolute beginners (and moderately experienced users) to enhance their ability to use the main job scheduler, SLURM.<br /> <br /> The slides for this course can be found here:<br /> <br /> [[File:Connecting_with_Secure_Shell_to_the_HPC_20170606.pdf | Basic introduction to Linux]]<br /> <br /> [[File:Submitting_and_monitoring_jobs_on_the_HPC_20170602.pdf | Submitting and Monitoring Jobs]]<br /> <br /> == Old Courses ==<br /> * [http://www.basgen.nl/sdac/ Sequence Data Analysis Course (Dec. 2012)]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1628 2015-11-12T13:40:03Z

<p>Vande018: /* Recipe */</p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC<br /> <br /> ==Definition==<br /> '''Checkpointing''': Saving the program's state at a checkpoint with the aim to restart it from that point in case of (un)planned stop of failure.<br /> <br /> It is interesting for, e.g., long jobs that could be (un)voluntary killed, or jobs running on unstable computing systems.<br /> <br /> ==Two types of program==<br /> ===The code is accessible===<br /> ====Recipe====<br /> Modify the code to implement the following recipe:<br /> <br /> &lt;source lang=text&gt;<br /> 1. Look for a state file that includes all imformation required to restore the state when the program <br /> was stopped.<br /> 2. If it exists, read it and restore the state. Else, create an intial state.<br /> 3. Periodically save the state to the state file.<br /> &lt;/source&gt;<br /> <br /> This recipe is applicable to several languages (e.g., R, Python, Matlab, Fortran, C, shell,...). Also, the checkpointing of parallel programs is easier after a global synchronization.&lt;br /&gt;<br /> The checkpointing requires:&lt;br /&gt;<br /> * some efforts to write some additional code;<br /> * some memory (e.g. for a state file). One must be careful to what is saved;<br /> * some time (e.g., to write the state file). Therefore, checkpointing too often must be avoided. Also, SLURM and other software features can be used to checkpoint at some specific points.<br /> <br /> ===The code is not accessible===<br /> Many software we used are checkpointable:&lt;br /&gt;<br /> * If it is the case, the (SLURM) script should be adapt to use this advantage. <br /> * If the software is really not checkpointable, some software are available to checkpoint existing programs. One of them is DMTCP (Distributed MultiThreaded CheckPointing; [http://dmtcp.sourceforge.net/ DMTCP]). The SLURM script must be modified to use it efficiently on the B4F HPC.</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1627 2015-11-12T13:39:23Z

<p>Vande018: /* Recipe */</p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC<br /> <br /> ==Definition==<br /> '''Checkpointing''': Saving the program's state at a checkpoint with the aim to restart it from that point in case of (un)planned stop of failure.<br /> <br /> It is interesting for, e.g., long jobs that could be (un)voluntary killed, or jobs running on unstable computing systems.<br /> <br /> ==Two types of program==<br /> ===The code is accessible===<br /> ====Recipe====<br /> Modify the code to implement the following recipe:<br /> <br /> &lt;source lang=text&gt;<br /> 1. Look for a state file that includes all imformation required to restore the state when the program <br /> was stopped.<br /> 2. If it exists, read it and restore the state. Else, create an intial state.<br /> 3. Periodically save the state to the state file.<br /> &lt;/source&gt;<br /> <br /> This recipe is applicable to several languages (e.g., R, Python, Matlab, Fortran, C, shell,...). Also, the checkpointing of parallel programs is easier after a global synchronization.&lt;br /&gt;<br /> The checkpointing requires some efforts:&lt;br /&gt;<br /> * to write some additional code;<br /> * some memory (e.g. for a state file). One must be careful to what is saved;<br /> * some time (e.g., to write the state file). Therefore, checkpointing too often must be avoided. Also, SLURM and other software features can be used to checkpoint at some specific points.<br /> <br /> ===The code is not accessible===<br /> Many software we used are checkpointable:&lt;br /&gt;<br /> * If it is the case, the (SLURM) script should be adapt to use this advantage. <br /> * If the software is really not checkpointable, some software are available to checkpoint existing programs. One of them is DMTCP (Distributed MultiThreaded CheckPointing; [http://dmtcp.sourceforge.net/ DMTCP]). The SLURM script must be modified to use it efficiently on the B4F HPC.</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1626 2015-11-12T13:35:28Z

<p>Vande018: /* The code is not accessible */</p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC<br /> <br /> ==Definition==<br /> '''Checkpointing''': Saving the program's state at a checkpoint with the aim to restart it from that point in case of (un)planned stop of failure.<br /> <br /> It is interesting for, e.g., long jobs that could be (un)voluntary killed, or jobs running on unstable computing systems.<br /> <br /> ==Two types of program==<br /> ===The code is accessible===<br /> ====Recipe====<br /> Modify the code to implement the following recipe:<br /> <br /> 1. Look for a state file that includes all imformation required to restore the state when the program was stopped.&lt;br /&gt;<br /> 2. If it exists, read it and restore the state. Else, create an intial state.&lt;br /&gt;<br /> 3. Periodically save the state to the state file.<br /> <br /> This recipe is applicable to several languages (e.g., R, Python, Matlab, Fortran, C, shell,...). Also, the checkpointing of parallel programs is easier after a global synchronization.&lt;br /&gt;<br /> The checkpointing requires some efforts:&lt;br /&gt;<br /> * to write some additional code;<br /> * some memory (e.g. for a state file). One must be careful to what is saved;<br /> * some time (e.g., to write the state file). Therefore, checkpointing too often must be avoided. Also, SLURM and other software features can be used to checkpoint at some specific points.<br /> <br /> <br /> ===The code is not accessible===<br /> Many software we used are checkpointable:&lt;br /&gt;<br /> * If it is the case, the (SLURM) script should be adapt to use this advantage. <br /> * If the software is really not checkpointable, some software are available to checkpoint existing programs. One of them is DMTCP (Distributed MultiThreaded CheckPointing; [http://dmtcp.sourceforge.net/ DMTCP]). The SLURM script must be modified to use it efficiently on the B4F HPC.</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1625 2015-11-12T13:34:19Z

<p>Vande018: </p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC<br /> <br /> ==Definition==<br /> '''Checkpointing''': Saving the program's state at a checkpoint with the aim to restart it from that point in case of (un)planned stop of failure.<br /> <br /> It is interesting for, e.g., long jobs that could be (un)voluntary killed, or jobs running on unstable computing systems.<br /> <br /> ==Two types of program==<br /> ===The code is accessible===<br /> ====Recipe====<br /> Modify the code to implement the following recipe:<br /> <br /> 1. Look for a state file that includes all imformation required to restore the state when the program was stopped.&lt;br /&gt;<br /> 2. If it exists, read it and restore the state. Else, create an intial state.&lt;br /&gt;<br /> 3. Periodically save the state to the state file.<br /> <br /> This recipe is applicable to several languages (e.g., R, Python, Matlab, Fortran, C, shell,...). Also, the checkpointing of parallel programs is easier after a global synchronization.&lt;br /&gt;<br /> The checkpointing requires some efforts:&lt;br /&gt;<br /> * to write some additional code;<br /> * some memory (e.g. for a state file). One must be careful to what is saved;<br /> * some time (e.g., to write the state file). Therefore, checkpointing too often must be avoided. Also, SLURM and other software features can be used to checkpoint at some specific points.<br /> <br /> <br /> ===The code is not accessible===<br /> Many software we used are checkpointable. If it is the case, the (SLURM) script should be adapt to use this advantage. If the software is really not checkpointable, some software are available to checkpoint existing programs. One of them is DMTCP (Distributed MultiThreaded CheckPointing; [http://dmtcp.sourceforge.net/ DMTCP]). The SLURM script must be modified to use it effeciently on the B4F HPC.</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1624 2015-11-12T13:26:51Z

<p>Vande018: </p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC<br /> <br /> ==Definition==<br /> '''Checkpointing''': Saving the program's state at a checkpoint with the aim to restart it from that point in case of (un)planned stop of failure.<br /> <br /> It is interesting for, e.g., long jobs that could be (un)voluntary killed, or jobs running on unstable computing systems.<br /> <br /> ==Two types of program==<br /> ===The code is accessible===<br /> ====Recipe====<br /> Modify the code to implement the following recipe:<br /> <br /> 1. Look for a state file that includes all imformation required to restore the state when the program was stopped.&lt;br /&gt;<br /> 2. If it exists, read it and restore the state. Else, create an intial state.&lt;br /&gt;<br /> 3. Periodically save the state to the state file.<br /> <br /> This recipe is applicable to several languages (e.g., R, Python, Matlab, Fortran, C, shell,...). Also, the checkpointing of parallel programs is easier after a global synchronization.&lt;br /&gt;<br /> The checkpointing requires some efforts:&lt;br /&gt;<br /> * to write some additional code;<br /> * some memory (e.g. for a state file). One must be careful to what is saved;<br /> * some time (e.g., to write the state file). Therefore, checkpointing too often must be avoided. Also, SLURM and other software features can be used to checkpoint at some specific points.<br /> <br /> <br /> ===The code is not accessible===</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1623 2015-11-12T13:21:22Z

<p>Vande018: </p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC<br /> <br /> ==Definition==<br /> '''Checkpointing''': Saving the program's state at a checkpoint with the aim to restart it from that point in case of (un)planned stop of failure.<br /> <br /> It is interesting for, e.g., long jobs that could be (un)voluntary killed, or jobs running on unstable computing systems.<br /> <br /> ==Two types of program==<br /> ===The code is accessible===<br /> ====Recipe====<br /> Modify the code to implement the following recipe:<br /> <br /> 1. Look for a state file that includes all imformation required to restore the state when the program was stopped.&lt;br /&gt;<br /> 2. If it exists, read it and restore the state. Else, create an intial state.&lt;br /&gt;<br /> 3. Periodically save the state to the state file.<br /> <br /> ===The code is not accessible===</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1622 2015-11-12T13:09:56Z

<p>Vande018: </p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC: [[Media:checkwiki.pdf]]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpoint&diff=1621 2015-11-12T13:02:03Z

<p>Vande018: Vande018 moved page Checkpoint to Checkpointing</p> <hr /> <div>#REDIRECT [[Checkpointing]]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1620 2015-11-12T13:02:03Z

<p>Vande018: Vande018 moved page Checkpoint to Checkpointing</p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Bioinformatics_tips_tricks_workflows&diff=1619 2015-11-12T13:01:10Z

<p>Vande018: /* A list of tutorials, workflows, and recipes */</p> <hr /> <div>This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts).<br /> <br /> == A list of tutorials, workflows, and recipes ==<br /> * [[Mapping_reads_with_Mosaik | Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly]]<br /> * [[convert_fastq_to_fasta | A Perl script to convert fastq to fasta file format]]<br /> * [[Mapping Pair-end reads with Stampy]]<br /> * [[making_slices_from_BAM_files | Create slices from a collection of BAM files ]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[ssh_without_password | ssh without password]]<br /> * [[Create_shortcut_log-in_command | Create a shortcut for the ssh log-in command]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[command_line_tricks_for_manipulating_fastq | Command-line tricks for manipulating fastq files]]<br /> * [[assemble_mitochondrial_genomes_from_short_read_data | Assemble mitochondrial genomes from whole-genome short-read data]]<br /> * [[1000Bulls_mapping_pipeline_at_ABGC | 1000 Bulls mapping pipeline at ABGC]]<br /> * [[ABGSA | Animal Breeding and Genomics Sequence Archives (ABGSA)]]<br /> * [[Short_read_mapping_pipeline_pig | Pig mapping pipeline at ABGC]]<br /> * [[Extract_noncall_snps_from_soy | Extract a set of pig SNPs not called in a control sample (soybean)]]<br /> * [[calculate_corrected_theta_from_resequencing_data | Calculate nucleotide diversity (theta) corrected for sequencing depth]]<br /> * [[RNA-seq analysis | RNA-seq analysis with Tophat]]<br /> * [[Variant_annotation_tutorial | Variant annotation tutorial]]<br /> * [[issues_asreml | Issues with ASReml]]<br /> * [[Checkpointing | Checkpointing]]<br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F Cluster]]<br /> <br /> == External links ==<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Checkpointing&diff=1618 2015-11-12T13:00:39Z

<p>Vande018: Created page with &quot;Some recipes and tips for checkpointing on the B4F HPC&quot;</p> <hr /> <div>Some recipes and tips for checkpointing on the B4F HPC</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Bioinformatics_tips_tricks_workflows&diff=1617 2015-11-12T12:58:38Z

<p>Vande018: /* A list of tutorials, workflows, and recipes */</p> <hr /> <div>This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts).<br /> <br /> == A list of tutorials, workflows, and recipes ==<br /> * [[Mapping_reads_with_Mosaik | Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly]]<br /> * [[convert_fastq_to_fasta | A Perl script to convert fastq to fasta file format]]<br /> * [[Mapping Pair-end reads with Stampy]]<br /> * [[making_slices_from_BAM_files | Create slices from a collection of BAM files ]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[ssh_without_password | ssh without password]]<br /> * [[Create_shortcut_log-in_command | Create a shortcut for the ssh log-in command]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[command_line_tricks_for_manipulating_fastq | Command-line tricks for manipulating fastq files]]<br /> * [[assemble_mitochondrial_genomes_from_short_read_data | Assemble mitochondrial genomes from whole-genome short-read data]]<br /> * [[1000Bulls_mapping_pipeline_at_ABGC | 1000 Bulls mapping pipeline at ABGC]]<br /> * [[ABGSA | Animal Breeding and Genomics Sequence Archives (ABGSA)]]<br /> * [[Short_read_mapping_pipeline_pig | Pig mapping pipeline at ABGC]]<br /> * [[Extract_noncall_snps_from_soy | Extract a set of pig SNPs not called in a control sample (soybean)]]<br /> * [[calculate_corrected_theta_from_resequencing_data | Calculate nucleotide diversity (theta) corrected for sequencing depth]]<br /> * [[RNA-seq analysis | RNA-seq analysis with Tophat]]<br /> * [[Variant_annotation_tutorial | Variant annotation tutorial]]<br /> * [[issues_asreml | Issues with ASReml]]<br /> * [[checkpoint | Checkpointing]]<br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F Cluster]]<br /> <br /> == External links ==<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Issues_asreml&diff=1607 2015-08-19T11:39:33Z

<p>Vande018: </p> <hr /> <div>Issues with ASReml on the HPC and possible solutions<br /> <br /> == Issue with the environment variable DISPLAY ==<br /> <br /> '''Issue'''<br /> <br /> Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with (some versions of) ASReml.<br /> <br /> <br /> '''Solution 1'''<br /> <br /> If you don't need a X11 server, you can disable it.<br /> <br /> <br /> '''Solution 2'''<br /> <br /> You can add in the script, before the line for ASReml, the following line:<br /> <br /> &lt;source lang='bash'&gt;<br /> export DISPLAY=' '<br /> &lt;/source&gt;</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Issues_asreml&diff=1606 2015-08-19T11:39:06Z

<p>Vande018: </p> <hr /> <div>Issues with ASReml on the HPC and possible solutions<br /> <br /> == Issue with the environment variable DISPLAY ==<br /> <br /> '''Issue'''<br /> <br /> Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with ASReml.<br /> <br /> <br /> '''Solution 1'''<br /> <br /> If you don't need a X11 server, you can disable it.<br /> <br /> <br /> '''Solution 2'''<br /> <br /> You can add in the script, before the line for ASReml, the following line:<br /> <br /> &lt;source lang='bash'&gt;<br /> export DISPLAY=' '<br /> &lt;/source&gt;</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Issues_asreml&diff=1605 2015-08-19T11:38:51Z

<p>Vande018: </p> <hr /> <div>Issues with ASReml on the HPC and possible solutions<br /> <br /> == Issue with the environment variable DISPLAY ==<br /> <br /> '''Issue'''<br /> <br /> Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with ASReml.<br /> <br /> '''Solution 1'''<br /> <br /> If you don't need a X11 server, you can disable it.<br /> <br /> <br /> <br /> '''Solution 2'''<br /> <br /> You can add in the script, before the line for ASReml, the following line:<br /> <br /> &lt;source lang='bash'&gt;<br /> export DISPLAY=' '<br /> &lt;/source&gt;</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Issues_asreml&diff=1604 2015-08-19T11:38:39Z

<p>Vande018: /* Issue with the environment variable DISPLAY */</p> <hr /> <div>Issues with ASReml on the HPC and possible solutions<br /> <br /> == Issue with the environment variable DISPLAY ==<br /> <br /> '''Issue'''<br /> Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with ASReml.<br /> <br /> '''Solution 1'''<br /> <br /> If you don't need a X11 server, you can disable it.<br /> <br /> <br /> <br /> '''Solution 2'''<br /> <br /> You can add in the script, before the line for ASReml, the following line:<br /> <br /> &lt;source lang='bash'&gt;<br /> export DISPLAY=' '<br /> &lt;/source&gt;</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Issues_asreml&diff=1603 2015-08-19T11:38:25Z

<p>Vande018: </p> <hr /> <div>Issues with ASReml on the HPC and possible solutions<br /> <br /> == Issue with the environment variable DISPLAY ==<br /> <br /> '''Issue'''<br /> Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with ASReml.<br /> <br /> '''Solution 1'''<br /> <br /> If you don't need a X11 server, you can disable it.<br /> <br /> '''Solution 2'''<br /> <br /> You can add in the script, before the line for ASReml, the following line:<br /> <br /> &lt;source lang='bash'&gt;<br /> export DISPLAY=' '<br /> &lt;/source&gt;</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Issues_asreml&diff=1602 2015-08-19T11:37:07Z

<p>Vande018: </p> <hr /> <div>Issues with ASReml on the HPC and possible solutions<br /> <br /> == Issue with the environment variable DISPLAY ==<br /> <br /> '''Issue'''<br /> Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with ASReml.<br /> <br /> '''Solution 1'''<br /> If you don't need a X11 server, you can disable it.<br /> <br /> '''Solution 2'''<br /> You can add in the script, before the line for ASReml, the following line:<br /> <br /> &lt;source lang='bash'&gt;<br /> export DISPLAY=' '<br /> &lt;/source&gt;</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Issues_asreml&diff=1601 2015-08-19T11:35:09Z

<p>Vande018: Created page with &quot;Issues with ASReml on the HPC and possible solutions == Issue with the environment variable DISPLAY == Some terminals for Windows (e.g., MobaXterm) set the environment varia...&quot;</p> <hr /> <div>Issues with ASReml on the HPC and possible solutions<br /> <br /> == Issue with the environment variable DISPLAY ==<br /> <br /> Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with ASReml.<br /> <br /> Solution 1:<br /> If you don't need a X11 server, you can disable it.<br /> <br /> Solution 2:<br /> You can add in the script, before the line for ASReml, the following line:<br /> <br /> &lt;source lang='bash'&gt;<br /> export DISPLAY=' '<br /> &lt;/source&gt;</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Bioinformatics_tips_tricks_workflows&diff=1600 2015-08-19T11:21:54Z

<p>Vande018: /* A list of tutorials, workflows, and recipes */</p> <hr /> <div>This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts).<br /> <br /> == A list of tutorials, workflows, and recipes ==<br /> * [[Mapping_reads_with_Mosaik | Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly]]<br /> * [[convert_fastq_to_fasta | A Perl script to convert fastq to fasta file format]]<br /> * [[Mapping Pair-end reads with Stampy]]<br /> * [[making_slices_from_BAM_files | Create slices from a collection of BAM files ]]<br /> * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]<br /> * [[ssh_without_password | ssh without password]]<br /> * [[Create_shortcut_log-in_command | Create a shortcut for the ssh log-in command]]<br /> * [[Installing_R_packages_locally | Installing R packages locally]]<br /> * [[command_line_tricks_for_manipulating_fastq | Command-line tricks for manipulating fastq files]]<br /> * [[assemble_mitochondrial_genomes_from_short_read_data | Assemble mitochondrial genomes from whole-genome short-read data]]<br /> * [[1000Bulls_mapping_pipeline_at_ABGC | 1000 Bulls mapping pipeline at ABGC]]<br /> * [[ABGSA | Animal Breeding and Genomics Sequence Archives (ABGSA)]]<br /> * [[Short_read_mapping_pipeline_pig | Pig mapping pipeline at ABGC]]<br /> * [[Extract_noncall_snps_from_soy | Extract a set of pig SNPs not called in a control sample (soybean)]]<br /> * [[calculate_corrected_theta_from_resequencing_data | Calculate nucleotide diversity (theta) corrected for sequencing depth]]<br /> * [[RNA-seq analysis | RNA-seq analysis with Tophat]]<br /> * [[Variant_annotation_tutorial | Variant annotation tutorial]]<br /> * [[issues_asreml | Issues with ASReml]]<br /> <br /> == See also ==<br /> * [[B4F_cluster | B4F Cluster]]<br /> <br /> == External links ==<br /> * [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Create_shortcut_log-in_command&diff=1436 2015-02-19T09:59:51Z

<p>Vande018: </p> <hr /> <div>It can be very tedious to have to type full command to log into a remote machine using the secure shell (ssh) when a remote machine is used often.<br /> <br /> == Add a custom command to the .bashrc ==<br /> A simple solution is to add a custom command to the .basrc. Open the .bashrc (which is in the root of home directory) using any plain text editor. E.g.:<br /> &lt;source lang='bash'&gt;<br /> vi $HOME/.bashrc<br /> &lt;/source&gt;<br /> <br /> Then, using the &lt;code&gt;alias&lt;/code&gt; function, define a new function derived from the &lt;code&gt;ssh&lt;/code&gt; command and your personal credentials:<br /> &lt;source lang='bash'&gt;<br /> alias lx7=&quot;ssh username@scomp1095.wurnet.nl&quot;<br /> alias hpc=&quot;ssh username@nfs01.hpcagrogenomics.wur.nl&quot;<br /> &lt;/source&gt;<br /> <br /> The new function will be available from next login, therefore log out of the active terminal and log back in. From the freshly opened terminal, issuing the following command:<br /> &lt;source lang='bash'&gt;<br /> lx7<br /> &lt;/source&gt;<br /> should give you direct access to &lt;code&gt;scomp1095&lt;/code&gt;, for instance. If you do this in combination with a [[ssh_without_password | passwordless setup]], you will not even be prompted for a password.<br /> <br /> == Using a ssh config file ==<br /> Instead of using the alias function, it is possible to use a ssh config file. The ssh config file can be found at $HOME/.ssh/config .<br /> If the ssh config file does not exist, you can create it with, e.g.,:<br /> &lt;source lang='bash'&gt;<br /> touch $HOME/.ssh.config <br /> &lt;/source&gt;<br /> If the ssh config file exists, you can add the different options you use to log in of the different servers/clusters. For example, for the B4F HPC, you can add:<br /> <br /> &lt;source lang='bash'&gt;<br /> Host hpc<br /> Hostname nfs01.hpcagrogenomics.wur.nl<br /> User username<br /> IdentityFile PATH_TO_PRIVATE_KEY (if applicable)<br /> ForwardX11 yes (if applicable)<br /> &lt;/source&gt;<br /> <br /> After the addition to the ssh congig file, you can log in as follows:<br /> &lt;source lang='bash'&gt;<br /> ssh hpc <br /> &lt;/source&gt;<br /> <br /> You may add to the ssh config file several configurations for the same or several clusters. For example, for the two aliases in the section [[Add a custom command to the .bashrc | Add a custom command to the .bashrc ]], you can add the following lines to your ssh config file:<br /> &lt;source lang='bash'&gt;<br /> Host scomp<br /> HostName scomp1095.wurnet.nl<br /> User username<br /> Host hpc<br /> Hostname nfs01.hpcagrogenomics.wur.nl<br /> User username<br /> &lt;/source&gt;<br /> <br /> For more information on the possible different options for the ssh config file, you may consult the [http://linux.die.net/man/5/ssh_config man page].<br /> <br /> == See also ==<br /> * [[ssh_without_password | ssh without password]]<br /> * [[Lx6_and_Lx7_compute_nodes | Lx6 and Lx7 compute nodes]]<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> <br /> == External links ==</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Create_shortcut_log-in_command&diff=1435 2015-02-19T09:56:25Z

<p>Vande018: /* Using a ssh config file */</p> <hr /> <div>It can be very tedious to have to type full command to log into a remote machine using the secure shell (ssh) when a remote machine is used often.<br /> <br /> == Add a custom command to the .bashrc ==<br /> A simple solution is to add a custom command to the .basrc. Open the .bashrc (which is in the root of home directory) using any plain text editor. E.g.:<br /> &lt;source lang='bash'&gt;<br /> vi $HOME/.bashrc<br /> &lt;/source&gt;<br /> <br /> Then, using the &lt;code&gt;alias&lt;/code&gt; function, define a new function derived from the &lt;code&gt;ssh&lt;/code&gt; command and your personal credentials:<br /> &lt;source lang='bash'&gt;<br /> alias lx7=&quot;ssh username@scomp1095.wurnet.nl&quot;<br /> alias hpc=&quot;ssh username@nfs01.hpcagrogenomics.wur.nl&quot;<br /> &lt;/source&gt;<br /> <br /> The new function will be available from next login, therefore log out of the active terminal and log back in. From the freshly opened terminal, issuing the following command:<br /> &lt;source lang='bash'&gt;<br /> lx7<br /> &lt;/source&gt;<br /> should give you direct access to &lt;code&gt;scomp1095&lt;/code&gt;, for instance. If you do this in combination with a [[ssh_without_password | passwordless setup]], you will not even be prompted for a password.<br /> <br /> == Using a ssh config file ==<br /> Instead of using the alias function, it is possible to use a ssh config file. The ssh config file can be found at $HOME/.ssh/config .<br /> If the ssh config file does not exist, you can create it with, e.g.,:<br /> &lt;source lang='bash'&gt;<br /> touch $HOME/.ssh.config <br /> &lt;/source&gt;<br /> If the ssh config file exists, you can add the different options you use to log in of the different servers/clusters. For example, for the B4F HPC, you can add:<br /> <br /> &lt;source lang='bash'&gt;<br /> Host hpc<br /> Hostname nfs01.hpcagrogenomics.wur.nl<br /> User username<br /> IdentityFile PATH_TO_PRIVATE_KEY (if applicable)<br /> ForwardX11 yes (if applicable)<br /> &lt;/source&gt;<br /> <br /> After the addition to the ssh congig file, you can log in as follows:<br /> &lt;source lang='bash'&gt;<br /> ssh hpc <br /> &lt;/source&gt;<br /> <br /> You may add to the ssh config file several configurations for the same or several clusters.<br /> For more information on the possible different options for the ssh config file, you may consult the [http://linux.die.net/man/5/ssh_config man page].<br /> <br /> == See also ==<br /> * [[ssh_without_password | ssh without password]]<br /> * [[Lx6_and_Lx7_compute_nodes | Lx6 and Lx7 compute nodes]]<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> <br /> == External links ==</div>

Vande018 https://wiki.anunna.wur.nl/index.php?title=Create_shortcut_log-in_command&diff=1434 2015-02-19T09:55:24Z

<p>Vande018: </p> <hr /> <div>It can be very tedious to have to type full command to log into a remote machine using the secure shell (ssh) when a remote machine is used often.<br /> <br /> == Add a custom command to the .bashrc ==<br /> A simple solution is to add a custom command to the .basrc. Open the .bashrc (which is in the root of home directory) using any plain text editor. E.g.:<br /> &lt;source lang='bash'&gt;<br /> vi $HOME/.bashrc<br /> &lt;/source&gt;<br /> <br /> Then, using the &lt;code&gt;alias&lt;/code&gt; function, define a new function derived from the &lt;code&gt;ssh&lt;/code&gt; command and your personal credentials:<br /> &lt;source lang='bash'&gt;<br /> alias lx7=&quot;ssh username@scomp1095.wurnet.nl&quot;<br /> alias hpc=&quot;ssh username@nfs01.hpcagrogenomics.wur.nl&quot;<br /> &lt;/source&gt;<br /> <br /> The new function will be available from next login, therefore log out of the active terminal and log back in. From the freshly opened terminal, issuing the following command:<br /> &lt;source lang='bash'&gt;<br /> lx7<br /> &lt;/source&gt;<br /> should give you direct access to &lt;code&gt;scomp1095&lt;/code&gt;, for instance. If you do this in combination with a [[ssh_without_password | passwordless setup]], you will not even be prompted for a password.<br /> <br /> == Using a ssh config file ==<br /> Instead of using the alias function, it is possible to use a ssh config file. The ssh config file can be found at $HOME/.ssh/config .<br /> If the ssh config file does not exist, you can create it with, e.g.,:<br /> &lt;source lang='bash'&gt;<br /> touch $HOME/.ssh.config <br /> &lt;/source&gt;<br /> If the ssh config file exists, you can add the different options you use to log in of the different servers/clusters. For example, for the B4F HPC, you can add:<br /> <br /> &lt;source lang='bash'&gt;<br /> Host hpc<br /> Hostname nfs01.hpcagrogenomics.wur.nl<br /> User username<br /> IdentityFile PATH_TO_PRIVATE_KEY (if applicable)<br /> ForwardX11 yes (if applicable)<br /> &lt;/source&gt;<br /> <br /> After the addition to the ssh congig file, you can log in as follows:<br /> &lt;source lang='bash'&gt;<br /> ssh hpc <br /> &lt;/source&gt;<br /> <br /> You may add to the ssh config file several configurations for the same or several clusters.<br /> For more information on the possible different options for the ssh config file, you may consult the [http://linux.die.net/man/5/ssh_config man page].<br /> <br /> <br /> == See also ==<br /> * [[ssh_without_password | ssh without password]]<br /> * [[Lx6_and_Lx7_compute_nodes | Lx6 and Lx7 compute nodes]]<br /> * [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]<br /> <br /> == External links ==</div>

Vande018