Difference between revisions of "Biocomputingpage"

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--></style></head><body lang=EN-US link="#0563C1" vlink="#954F72"><div class=WordSection1 dir=RTL><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><u>How to set up a unix account:</u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>To obtain a unix user name and password, create an account by
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registering at <a href="https://registrar.cs.huji.ac.il/account">https://registrar.cs.huji.ac.il/account</a>.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><u>Connecting to the hm server:</u><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>Before connecting to the hm server, an SSH connection needs to be set
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up. Instructions for set-up can be found at <a
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href="http://wiki.cs.huji.ac.il/wiki/Connecting_from_outside">http://wiki.cs.huji.ac.il/wiki/Connecting_from_outside</a>.
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<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>Every time you connect to the system, you will need to use a One-Time
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password (OTP) in addition to your unix (IDng) password. Instructions for
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obtaining OTPs can be found at <a
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href="http://wiki.cs.huji.ac.il/wiki/Password_and_OTP">http://wiki.cs.huji.ac.il/wiki/Password_and_OTP</a>.<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>It is helpful to set up an FTP connection for easy file transfer between
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your desktop computer and the server. To do this with MobaXterm: <p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>Create a new SFTP session by clicking on 'Session' and then 'SFTP'. Fill
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in the basic settings so that remote host = localhost, username = <your unix
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user name>, and the port = 9001. For example:<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><img border=0 width=554 height=437 id="Picture 1"
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src="wikiWebF_files/image001.jpg"><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>You will then need to create an SSH tunnel by clicking on 'Tunneling'
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and then 'New SSH Tunnel', and fill in the fields (using your unix user name)
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as follows:<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><img border=0 width=553 height=359 id="Picture 2"
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src="wikiWebF_files/image002.jpg"><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>Before you start the transfer you will need to: <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>1 - start the tunnel by clicking on 'Tunneling' and press  the <img
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border=0 width=23 height=25 id="Picture 3" src="wikiWebF_files/image003.png"> button
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<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>2- provide an OTP to open the tunnel <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>3- start the FTP connection by double clicking on the SFTP session <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>4- enter your unix password <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>The connection will eventually time out (you will see that the <img
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border=0 width=23 height=25 id="Picture 4" src="wikiWebF_files/image003.png"> button
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will no longer be pressed) after which you will need to re-do steps 1-4 to
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re-open it. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><u>Basic linux commands:</u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>For an introduction to some basic linux commands, take a look at the
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Intro_hm_cluster.pptx presentation.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><u><span style='text-decoration:none'> </span></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><u>Understanding the file system:</u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>The file system is divided into two main directories – icore and lustre.
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<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>Your icore directory can be found in ''/cs/icore/<your unix user
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name>. ''Icore is backed up with snapshots so a few previous versions of
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all files will be saved even after they are modified/deleted (assuming that the
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file system is up and running), however it has limited space. '''Icore should
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be used mainly to store your scripts.''' You should keep a copy of your
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scripts on Git, which allows you to save different versions. To use Git to back
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up scripts, see <a href="http://wiki.cs.huji.ac.il/wiki/Github">here</a>. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>Your lustre directory can be found in ''/mnt/lustre/hms-01/fs01/<your
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unix user name>''. '''Lustre should be used mainly to store the data'''
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that you are currently working on as it is meant for quick and efficient
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computations. '''IMPORTANT:''''''lustre is not backed up! '''This means that
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files on lustre that are accidentally deleted will be lost forever, so please '''be
+
sure to back up all important files '''(e.g. on an external hard drive). <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>There are graphical interfaces that can make navigating the file system
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easier. For example, the nautilus file manager (can be opened with the command
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'nautilus >& /dev/null &') and gedit text editor ('gedit >&
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/dev/null &'). For more information, take a look at the
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Intro_hm_cluster.pptx presentation.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><u><span style='text-decoration:none'> </span></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'><u>Using slurm on the hm cluster:</u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>The hm cluster currently has 44 nodes on which jobs can run. Slurm is a
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job scheduler that decides which node(s) a job will run on based on the job's
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requested resources (e.g. number of cpus, amount of memory, etc…), the
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availability of idle nodes, and the priority of the user which depends on how
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many jobs were run in the past. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>All jobs should be submitted as sbatch scripts to slurm where they will
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be queued and will start running as soon as all of their requested resources
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become available.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>Some resource arguments that most users will want to tweak are:<div align=left dir=ltr>
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{| class=MsoTableGrid border=1 cellspacing=0 cellpadding=0 width=0  style='width:357.95pt;border-collapse:collapse;border:none'
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|- <td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>'''Argument
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'''<td width=75 valign=top style='width:57.55pt;border:solid windowtext 1.0pt;
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border-left:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>'''Default
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value'''<td width=88 valign=top style='width:66.6pt;border:solid windowtext 1.0pt;
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border-left:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>'''Maximum
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value'''<td width=94 valign=top style='width:71.2pt;border:solid windowtext 1.0pt;
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border-left:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>'''Description'''<td width=133 valign=top style='width:95.85pt;border:solid windowtext 1.0pt;
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border-left:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>'''Notes'''
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|- <td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
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border-top:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>-c,
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--cpus-per-task<td width=75 valign=top style='width:57.55pt;border-top:none;border-left:
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none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>2<td width=88 valign=top style='width:66.6pt;border-top:none;border-left:none;
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border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>32<td width=94 valign=top style='width:71.2pt;border-top:none;border-left:none;
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border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>number
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of cpus for job<td width=133 valign=top style='width:95.85pt;border-top:none;border-left:
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none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>Maximum
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depends on CPU used in cluster, hm I-CORE cluster is 32.
+
|- <td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
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border-top:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>--mem<td width=75 valign=top style='width:57.55pt;border-top:none;border-left:
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none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>50MB<td width=88 valign=top style='width:66.6pt;border-top:none;border-left:none;
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border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>~64GB or
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~128GB<td width=94 valign=top style='width:71.2pt;border-top:none;border-left:none;
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border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+
padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>memory
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allocation for job<td width=133 valign=top style='width:95.85pt;border-top:none;border-left:
+
none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>Depends
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on memory of nodes, we have nodes with 64GB and 128GB of memory, you can't
+
request all the memory since some is needed for the OS, if you want it all
+
and don't care which node you can use: MaxMemPerNode. See below for more
+
details.
+
|- <td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
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border-top:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>-t,
+
--time<td width=75 valign=top style='width:57.55pt;border-top:none;border-left:
+
none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+
padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>2 hours<td width=88 valign=top style='width:66.6pt;border-top:none;border-left:none;
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border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>31 days<td width=94 valign=top style='width:71.2pt;border-top:none;border-left:none;
+
border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>time
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limit for job<td width=133 valign=top style='width:95.85pt;border-top:none;border-left:
+
none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+
padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>Currently
+
31 days may be reverted to 21 days later.
+
|- <td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
+
border-top:none;padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>-N,
+
--nodes<td width=75 valign=top style='width:57.55pt;border-top:none;border-left:
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none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
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padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>1<td width=88 valign=top style='width:66.6pt;border-top:none;border-left:none;
+
border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+
padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
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text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>44<td width=94 valign=top style='width:71.2pt;border-top:none;border-left:none;
+
border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+
padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>number
+
of nodes to run job on<td width=133 valign=top style='width:95.85pt;border-top:none;border-left:
+
none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+
padding:0cm 5.4pt 0cm 5.4pt'><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed'>Currently
+
44, may be increased in the future, either due to additional hardware
+
purchases or reassigning of submit/test hosts to 'active duty' compute nodes.
+
|}</div><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>For more information on all sbatch arguments, e.g., the proper format
+
for writing time limits, etc…, read the <a
+
href="https://slurm.schedmd.com/sbatch.html">sbatch manual</a>.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u><span style='text-decoration:none'> </span></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>Submitting a job to the slurm queue:</u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>There are 2 general ways to submit jobs using sbatch:<p class=MsoListParagraph dir=LTR style='margin-top:0cm;margin-right:0cm;
+
margin-bottom:8.0pt;margin-left:36.0pt;text-align:left;text-indent:-18.0pt;
+
direction:ltr;unicode-bidi:embed'>1.<span style='font:7.0pt "Times New Roman"'>      
+
</span><span dir=LTR></span>one-liner<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Resources can be requested as arguments on the command line, for
+
example:<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;line-height:107%;font-family:"Courier New";
+
color:#222222'>sbatch -N 2 --mem 8GB --wrap script.sh</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'>The above command will submit ''script.sh'' as a job to slurm with
+
two nodes and 8GB of RAM requested. The --wrap argument is needed so that the
+
script (or command) is wrapped in an sbatch script.<p class=MsoNormal dir=LTR style='margin-top:0cm;margin-right:0cm;margin-bottom:
+
0cm;margin-left:18.0pt;margin-bottom:.0001pt;text-align:left;line-height:normal;
+
background:white;direction:ltr;unicode-bidi:embed'> <p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'>To run a command with arguments, you need to enclose the command and its
+
arguments in quotes, for example:<p class=MsoNormal dir=LTR style='margin-top:0cm;margin-right:0cm;margin-bottom:
+
0cm;margin-left:18.0pt;margin-bottom:.0001pt;text-align:left;line-height:normal;
+
background:white;direction:ltr;unicode-bidi:embed'> <pre dir=LTR style='background:white'><span style='color:#222222'>sbatch –o output.txt --wrap 'head -n 20 file.txt'</span></pre><pre
+
dir=LTR style='text-indent:18.0pt;background:white'><span style='color:#222222'> </span></pre><pre
+
dir=LTR style='background:white'><span style='font-size:11.0pt;font-family:
+
"Calibri",sans-serif'>The above code will submit the command 'head -n 20 file.txt' as a job to slurm and will write the output of the command (the first 20 lines of ''file.txt'') to the file ''output.txt''. </span></pre><p class=MsoNormal dir=LTR style='margin-left:90.0pt;text-align:left;
+
direction:ltr;unicode-bidi:embed'> <p class=MsoListParagraph dir=LTR style='margin-top:0cm;margin-right:0cm;
+
margin-bottom:8.0pt;margin-left:36.0pt;text-align:left;text-indent:-18.0pt;
+
direction:ltr;unicode-bidi:embed'>2.<span style='font:7.0pt "Times New Roman"'>      
+
</span><span dir=LTR></span>sbatch script (recommended)<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Resources can be requested by adding special argument comments to bash
+
scripts. These start with #SBATCH and then contain the sbatch argument, and
+
will be parsed by sbatch until the script starts, so an #SBATCH argument
+
written after the first command of the script will be ignored by sbatch. Here
+
is an example of a bash script called ''my-sbatch-script.sh'' with sbatch
+
arguments:<pre dir=LTR style='background:white'><span style='color:#222222'>#!/bin/bash</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH --mem 10GB</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>echo "hello world" </span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'># The following line will not be parsed by sbatch</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH --time 10</span></pre><p class=MsoNormal dir=LTR style='margin-left:90.0pt;text-align:left;
+
direction:ltr;unicode-bidi:embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The above script can then be submitted to the slurm queue from the
+
command line as follows:<pre dir=LTR style='background:white'><span style='color:#222222'>sbatch my-sbatch-script.sh</span></pre><p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
+
direction:ltr;unicode-bidi:embed'>'' ''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>''my-sbatch-script.sh'' will be submitted as a job to the slurm queue
+
with 10GB of RAM requested. The time limit for the job will be the default two
+
hours since the time parameter will not be parsed by sbatch as it is written
+
after a command in the script.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u><span style='text-decoration:none'> </span></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>Requesting resources:</u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Make sure that your job does not request more resources than the maximum
+
(please refer to table above). '''Jobs that request more than the maximum
+
number of resources will not run.'''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>'''Requests should be kept to as close to the needs of your job as
+
possible''' for two main reasons: <p class=MsoListParagraphCxSpFirst dir=LTR style='margin-top:0cm;margin-right:
+
0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-align:left;text-indent:-18.0pt;
+
direction:ltr;unicode-bidi:embed'>1-<span style='font:7.0pt "Times New Roman"'>     
+
</span><span dir=LTR></span>jobs are prioritized in the queue mainly based on
+
requested resources, meaning that the more resources requested, the longer the
+
job will take to start running since it needs to wait for all resources to become
+
available<p class=MsoListParagraphCxSpLast dir=LTR style='margin-top:0cm;margin-right:
+
0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-align:left;text-indent:-18.0pt;
+
direction:ltr;unicode-bidi:embed'>2-<span style='font:7.0pt "Times New Roman"'>     
+
</span><span dir=LTR></span> while a job is running, all of its allocated
+
resources will be unavailable to other users even if the job is not using them<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>'''Requesting multiple nodes:'''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Requesting multiple nodes for a specific job does '''not'''
+
automatically divide the job among the nodes. There are a few ways to use
+
multiple nodes simultaneously in order to save computation time: <p class=MsoListParagraphCxSpFirst dir=LTR style='margin-top:0cm;margin-right:
+
0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-align:left;text-indent:-18.0pt;
+
direction:ltr;unicode-bidi:embed'>1-<span style='font:7.0pt "Times New Roman"'>     
+
</span><span dir=LTR></span>using mpirun<p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-align:left;text-indent:-18.0pt;
+
direction:ltr;unicode-bidi:embed'>2-<span style='font:7.0pt "Times New Roman"'>     
+
</span><span dir=LTR></span>using srun <p class=MsoListParagraphCxSpLast dir=LTR style='margin-top:0cm;margin-right:
+
0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-align:left;text-indent:-18.0pt;
+
direction:ltr;unicode-bidi:embed'>3-<span style='font:7.0pt "Times New Roman"'>     
+
</span><span dir=LTR></span>using an outer submit script – this is recommended
+
as it is the simplest method  <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>1- using mpirun:<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>If you know that you are running a program that depends on OpenMPI, you
+
can use mpirun to run the program on multiple nodes in parallel – see the <a
+
href="https://www.mpi-forum.org/docs/">mpi manual</a> for more information.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>2- using srun:<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Srun can be used within an sbatch script to utilize a subset of the
+
total requested resources. It can be used to run a command using multiple nodes
+
in parallel which is most useful if you want to run a script/command on many
+
files at the same time, each as its own job on one node, for example:<pre dir=LTR style='background:white'><span style='color:#222222'>#!/bin/bash</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH -N 5</span></pre><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'> </span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>files=(file0
+
file1 file2 file3 file4)</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'> </span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>for
+
i in {0..4}</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>do    </span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;text-indent:36.0pt;line-height:normal;background:white;
+
direction:ltr;unicode-bidi:embed'><span style='font-size:10.0pt;font-family:
+
"Courier New";color:#222222'>srun -N 1 –o output.$i.txt head –n 20 ${files[$i]}
+
&</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>done</span><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The above script will allocate five nodes as requested, and then will
+
send five jobs to the slurm queue at the same time, each running on one node.
+
The output of each job (the first twenty lines of the corresponding file) will
+
be printed in the ''output.{i}.txt'' file. If you submit the above script as
+
a job without using the srun command, for example:<pre dir=LTR style='background:white'><span style='color:#222222'>#!/bin/bash</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH -N 5</span></pre><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'> </span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>files=(file0
+
file1 file2 file3 file4)</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'> </span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>for
+
i in {0..4}</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>do</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;text-indent:36.0pt;line-height:normal;background:white;
+
direction:ltr;unicode-bidi:embed'><span style='font-size:10.0pt;font-family:
+
"Courier New";color:#222222'>head –n 20 ${files[$i]} &</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>done</span><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Once the above job starts running, it will hold five nodes unavailable
+
to other users as requested, but it will only run on one node.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>3- using an outer submit script: <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The simplest way to run a script/command on many files at the same time,
+
each as its own job on one node, is by using a for loop in a script that
+
submits all of the jobs at once. For example:<pre dir=LTR style='background:white'><span style='color:#222222'>#!/bin/bash</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'> </span></pre><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>files=(file0
+
file1 file2 file3 file4)</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'> </span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>for
+
file in ${files[*]}</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>do</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;text-indent:36.0pt;line-height:normal;background:white;
+
direction:ltr;unicode-bidi:embed'><span style='font-size:10.0pt;font-family:
+
"Courier New";color:#222222'>sbatch head.sh $file </span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>done</span><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;background:white;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'> </span><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The above script loops through all files in the list 'files' and submits
+
the script ''head.sh'' (with 'file' as an argument) as an sbatch job. The ''head.sh''
+
script will contain the sbatch arguments needed to run on one file. For
+
example:<pre dir=LTR style='background:white'><span style='color:#222222'>#!/bin/bash</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH –o output.txt</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH –N 1</span></pre><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>file=$1
+
#first argument from outer script</span><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span style='font-size:10.0pt;font-family:"Courier New";color:#222222'>head
+
–n 20 $file</span><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The ''head.sh'' script will be run as a job on one node (based on the
+
sbatch arguments written in the script) on each of the 5 files in parallel. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>'''Requesting multiple cpus:'''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>If you are running a program that supports multithreading, you can
+
request multiple cpus (up to the maximum) and then run the program while
+
specifying the number of cpus you want it to use as a parameter. For example:<pre dir=LTR style='background:white'><span style='color:#222222'>#!/bin/bash</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH –c 32 #request 32 cpus</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH –o output.txt</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>sample=$1</span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>bowtie2 -p 32 -x $genome -U $sample -S $sam >& bowtie2.log</span></pre><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The above script can be submitted as a job that will run bowtie2 using
+
32 cpus on 'sample' (with the bowtie2 output saved in the file ''bowtie2.log'').<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>''' '''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>'''Requesting memory:'''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>If the amount of memory requested is not enough for the job, it will be
+
killed with an error message that the job exceeded the memory limit and you
+
will need to increase the memory request. There is currently no simple method
+
to know how much memory a job will need before it runs. Once an sbatch job is
+
running you can check its accounting information with the 'sacct' command. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>For more information, read the <a
+
href="http://wiki.cs.huji.ac.il/wiki/Slurm">CS slurm wiki</a>.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>FAQs </u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>1.  How do I check the status of my job?<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>By running the command 'squeue –u username' with your username you will
+
see all of your submitted jobs and their status (ST column). PD means your job
+
is pending in the queue waiting to start, and R means it is running. For a list
+
of all status codes, read the 'JOB STATE CODES' section of the <a
+
href="https://slurm.schedmd.com/squeue.html">squeue manual</a>.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>2.  How do I cancel a job?<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Jobs can be cancelled by running the command 'scancel jobid' where the
+
jobid is the number that slurm assigned your job when it was submitted which
+
you can see by running 'squeue –u username' and looking at the JOBID column.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>3.  Why is my job taking so long to start running?<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Jobs are prioritized in the slurm queue mainly based on the amount of
+
resources requested. The more resources your job requests, the longer it will
+
take to start running.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>4.  How much memory/cpus did my job actually use? <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>When a job is running, you can use the following commands to see its
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accounting information:<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>sacct – see the <a href="https://slurm.schedmd.com/sacct.html">sacct
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manual</a> for more details<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>sstat – see the <a href="https://slurm.schedmd.com/sstat.html">sstat
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manual</a> for more details<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>5.  Can I submit a job and tell it to run at a later time?<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'>You can tell a job what time you want it to start running with the
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parameter --begin:<pre dir=LTR style='background:white'><span style='color:#222222'>#SBATCH --begin HH:MM MM/DD/YY</span></pre><pre
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dir=LTR style='background:white'><span style='color:#222222'> </span></pre><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> Alternatively, you can add dependencies to your jobs so that, for
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example, job #2 will not start until job #1 satisfies the provided condition,
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by using the job id. This can be done in a bash script:<pre dir=LTR style='background:white'><span style='color:#222222'>#!/bin/bash</span></pre><pre
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dir=LTR style='background:white'><span style='color:#222222'>jobid1=$(sbatch job1.sh)      </span></pre><pre
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dir=LTR style='background:white'><span style='color:#222222'>sbatch –-dependency afterok:jobid1 job2.sh    </span></pre><pre
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dir=LTR style='background:white'><span style='color:#222222'> </span></pre><pre
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dir=LTR style='background:white'><span style='font-size:11.0pt;font-family:
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"Calibri",sans-serif'>The above script submits ''job1.sh'' as a job and saves jobid in the variable jobid1. It then submits ''job2.sh'' as a job only once job1 finishes running with an exit code of 0 as defined by the condition 'afterok'. For more information on possible conditions, etc… please refer to the </span><a
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href="https://slurm.schedmd.com/sbatch.html"><span style='font-size:11.0pt;
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font-family:"Calibri",sans-serif'>sbatch manual</span></a><span
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style='font-size:11.0pt;font-family:"Calibri",sans-serif'>.</span></pre><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
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embed'> </div></body></html>
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Latest revision as of 08:24, 9 July 2018