Difference between revisions of "Biocomputingpage"

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</style><![endif]--><!--[if gte mso 9]><xml><o:shapedefaults v:ext="edit" spidmax="1026"/></xml><![endif]--><!--[if gte mso 9]><xml><o:shapelayout v:ext="edit"><o:idmap v:ext="edit" data="1"/></o:shapelayout></xml><![endif]--></head><body lang=EN-US link="#0563C1" vlink="#954F72" style='tab-interval:36.0pt'><div class=WordSection1 dir=RTL><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>How to set up a <span class=SpellE><span class=GramE>unix</span></span>
+
account:<o:p></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>To obtain a <span class=SpellE><span class=GramE>unix</span></span> user
+
name and password, create an account by 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:
+
embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>Connecting to the <span class=SpellE>hm</span> server:<o:p></o:p></u><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Before connecting to the <span class=SpellE>hm</span> server, an SSH
+
connection needs to be set up. Instructions for set-up can be found at <a
+
href="http://wiki.cs.huji.ac.il/wiki/Connecting_from_outside">http://wiki.cs.huji.ac.il/wiki/Connecting_from_outside</a>.
+
<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Every time you connect to the system, you will need to use a One-Time
+
password (OTP) in addition to your <span class=SpellE><span class=GramE>unix</span></span>
+
(<span class=SpellE>IDng</span>) password. Instructions for obtaining OTPs can
+
be found at <a 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:
+
embed'><o:p> </o:p><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>It is helpful to set up an FTP connection for easy file transfer between
+
your desktop computer and the server. To do this with <span class=SpellE>MobaXterm</span>:
+
<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Create a new SFTP session by clicking on 'Session' and then 'SFTP'. Fill
+
in the basic settings so that remote host = localhost, username = <your <span
+
class=SpellE><span class=GramE>unix</span></span> user name>, and the port =
+
9001. For example:<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype id="_x0000_t75"
+
coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe"
+
filled="f" stroked="f"><v:stroke joinstyle="miter"/><v:formulas><v:f eqn="if lineDrawn pixelLineWidth 0"/><v:f eqn="sum @0 1 0"/><v:f eqn="sum 0 0 @1"/><v:f eqn="prod @2 1 2"/><v:f eqn="prod @3 21600 pixelWidth"/><v:f eqn="prod @3 21600 pixelHeight"/><v:f eqn="sum @0 0 1"/><v:f eqn="prod @6 1 2"/><v:f eqn="prod @7 21600 pixelWidth"/><v:f eqn="sum @8 21600 0"/><v:f eqn="prod @7 21600 pixelHeight"/><v:f eqn="sum @10 21600 0"/></v:formulas><v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/><o:lock v:ext="edit" aspectratio="t"/></v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1028" type="#_x0000_t75"
+
style='width:415.5pt;height:327.75pt;visibility:visible;mso-wrap-style:square'><v:imagedata src="wiki_files/image001.png" o:title=""/></v:shape><![endif]--><![if !vml]><img border=0 width=554 height=437
+
src="wiki_files/image006.jpg" v:shapes="Picture_x0020_1"><![endif]></span><span
+
style='mso-spacerun:yes'></span><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>You will then need to create an SSH tunnel by clicking on 'Tunneling'
+
and then 'New SSH Tunnel', and fill in the fields (using your <span
+
class=SpellE><span class=GramE>unix</span></span> user name) as follows:<p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_2"
+
o:spid="_x0000_i1027" type="#_x0000_t75" style='width:414.75pt;height:269.25pt;
+
visibility:visible;mso-wrap-style:square'><v:imagedata src="wiki_files/image003.png" o:title=""/></v:shape><![endif]--><![if !vml]><img border=0 width=553 height=359
+
src="wiki_files/image007.jpg" v:shapes="Picture_x0020_2"><![endif]></span><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Before you start the transfer you will need to: <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>1 - <span class=GramE>start</span> the tunnel by clicking on 'Tunneling'
+
and press<span style='mso-spacerun:yes'></span>the <span style='mso-no-proof:
+
yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_3" o:spid="_x0000_i1026"
+
type="#_x0000_t75" style='width:17.25pt;height:18.75pt;visibility:visible;
+
mso-wrap-style:square'><v:imagedata src="wiki_files/image005.png" o:title=""/></v:shape><![endif]--><![if !vml]><img border=0 width=23 height=25
+
src="wiki_files/image005.png" v:shapes="Picture_x0020_3"><![endif]></span><span
+
style='mso-spacerun:yes'></span>button <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>2- <span class=GramE>provide</span> an OTP to open the tunnel <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>3- <span class=GramE>start</span> the FTP connection by double clicking
+
on the SFTP session <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>4- <span class=GramE>enter</span> your <span class=SpellE>unix</span>
+
password <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The connection will eventually time out (you will see that the <span
+
style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
+
o:spid="_x0000_i1025" type="#_x0000_t75" style='width:17.25pt;height:18.75pt;
+
visibility:visible;mso-wrap-style:square'><v:imagedata src="wiki_files/image005.png" o:title=""/></v:shape><![endif]--><![if !vml]><img border=0 width=23 height=25
+
src="wiki_files/image005.png" v:shapes="Picture_x0020_4"><![endif]></span><span
+
style='mso-spacerun:yes'></span>button will no longer be pressed) after which
+
you will need to re-do steps 1-4 to re-open it. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>Basic <span class=SpellE>linux</span> commands:<o:p></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>For an introduction to some basic <span class=SpellE>linux</span>
+
commands, take a look at the Intro_hm_cluster.pptx presentation.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u><o:p><span style='text-decoration:none'> </span></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>Understanding the file system:<o:p></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The file system is divided into two main directories – <span
+
class=SpellE>icore</span> and <span class=SpellE>lustre</span>. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Your <span class=SpellE>icore</span> directory can be found in ''/<span
+
class=SpellE>cs</span>/<span class=SpellE>icore</span>/<your <span
+
class=SpellE><span class=GramE>unix</span></span> user name>. ''<span
+
class=SpellE>Icore</span> is backed up with snapshots so a few previous
+
versions of all files will be saved even after they are modified/deleted
+
(assuming that the file system is up and running), however it has limited
+
space. <span class=SpellE>'''Icore'''</span>''' should be used mainly to store
+
your scripts.''' You should keep a copy of your scripts on <span class=SpellE>Git</span>,
+
which allows you to save different versions. To use <span class=SpellE>Git</span>
+
to back 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:
+
embed'>Your <span class=SpellE>lustre</span> directory can be found in ''/<span
+
class=SpellE>mnt</span>/<span class=SpellE>lustre</span>/<span class=GramE>hms-</span>01/fs01/<your
+
<span class=SpellE>unix</span> user name>''. <span class=SpellE>'''Lustre'''</span>'''
+
should be used mainly to store the data''' that you are currently working on
+
as it is meant for quick and efficient computations. '''IMPORTANT:'''<span
+
class=SpellE>'''lustre'''</span>''' is not backed up! '''This means that
+
files on <span class=SpellE>lustre</span> 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:
+
embed'>There are graphical interfaces that can make navigating the file system
+
easier. For example, the nautilus file manager (can be opened with the command
+
'nautilus >& /dev/null &') and <span class=SpellE>gedit</span> text
+
editor ('<span class=SpellE>gedit</span> >& /dev/null &'). For more
+
information, take a look at the Intro_hm_cluster.pptx presentation.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u><o:p><span style='text-decoration:none'> </span></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>Using <span class=SpellE>slurm</span> on the <span class=SpellE>hm</span>
+
cluster:<o:p></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The <span class=SpellE>hm</span> cluster currently has 44 nodes on which
+
jobs can run. <span class=SpellE>Slurm</span> is a job scheduler that decides
+
which node(s) a job will run on based on the job's requested resources (e.g.
+
number of <span class=SpellE>cpus</span>, amount of memory, <span class=SpellE>etc</span>…),
+
the availability of idle nodes, and the priority of the user which depends on
+
how many jobs were run in the past. <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>All jobs should be submitted as <span class=SpellE>sbatch</span> scripts
+
to <span class=SpellE>slurm</span> where they will be queued and will start
+
running as soon as all of their requested resources become available.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Some resource arguments that most users will want to tweak are:<div align=left dir=ltr>
+
{| class=MsoTableGrid border=1 cellspacing=0 cellpadding=0 width=0  style='width:357.95pt;border-collapse:collapse;border:none;mso-border-alt:  solid windowtext .5pt;mso-yfti-tbllook:1184;mso-padding-alt:0cm 5.4pt 0cm 5.4pt'
+
|- style='mso-yfti-irow:0;mso-yfti-firstrow:yes'<td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
+
mso-border-alt:solid windowtext .5pt;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'>'''Argument
+
<o:p></o:p>'''<td width=75 valign=top style='width:57.55pt;border:solid windowtext 1.0pt;
+
border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:
+
solid windowtext .5pt;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'>'''Default
+
value<o:p></o:p>'''<td width=88 valign=top style='width:66.6pt;border:solid windowtext 1.0pt;
+
border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:
+
solid windowtext .5pt;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'>'''Maximum
+
value<o:p></o:p>'''<td width=94 valign=top style='width:71.2pt;border:solid windowtext 1.0pt;
+
border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:
+
solid windowtext .5pt;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'>'''Description<o:p></o:p>'''<td width=133 valign=top style='width:95.85pt;border:solid windowtext 1.0pt;
+
border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:
+
solid windowtext .5pt;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'>'''Notes<o:p></o:p>'''
+
|- style='mso-yfti-irow:1'<td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
+
border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
+
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'>-c, --<span
+
class=SpellE>cpus</span>-per-task<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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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<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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'>32<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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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 <span class=SpellE>cpus</span> 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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'>Maximum
+
depends on CPU used in cluster, <span class=SpellE>hm</span> I-CORE cluster
+
is 32.
+
|- style='mso-yfti-irow:2'<td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
+
border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
+
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'>--mem<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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'>50MB<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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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
+
~128GB<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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'>memory
+
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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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
+
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: <span class=SpellE>MaxMemPerNode</span>.
+
See below for more details.
+
|- style='mso-yfti-irow:3'<td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
+
border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
+
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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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;
+
border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'>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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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
+
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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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.
+
|- style='mso-yfti-irow:4;mso-yfti-lastrow:yes'<td width=88 valign=top style='width:66.75pt;border:solid windowtext 1.0pt;
+
border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
+
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'>-N,
+
--nodes<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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'>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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'>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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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;
+
mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
+
mso-border-alt:solid windowtext .5pt;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'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>For more information on all <span class=SpellE>sbatch</span> arguments,
+
e.g., the proper format for writing time limits, <span class=SpellE>etc</span>…,
+
read the <a href="https://slurm.schedmd.com/sbatch.html"><span class=SpellE>sbatch</span>
+
manual</a>.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u><o:p><span style='text-decoration:none'> </span></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>Submitting a job to the <span class=SpellE>slurm</span> queue:<o:p></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>There are 2 general ways to submit jobs using <span class=SpellE>sbatch</span>:<p class=MsoListParagraph dir=LTR style='margin-top:0cm;margin-right:0cm;
+
margin-bottom:8.0pt;margin-left:36.0pt;mso-add-space:auto;text-align:left;
+
text-indent:-18.0pt;mso-list:l0 level1 lfo1;direction:ltr;unicode-bidi:embed'><![if !supportLists]><span
+
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
+
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>      
+
</span></span></span><![endif]><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 class=SpellE><span class=GramE><span style='font-size:10.0pt;
+
line-height:107%;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>sbatch</span></span></span><span style='font-size:10.0pt;
+
line-height:107%;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'> -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;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
+
background:white;direction:ltr;unicode-bidi:embed'>The above command will
+
submit ''script.sh'' as a job to <span class=SpellE>slurm</span> with two
+
nodes and 8GB of RAM requested. The --wrap argument is needed so that the
+
script (or command) is wrapped in <span class=GramE>an</span><span
+
class=SpellE>sbatch</span> 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;
+
tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
+
background:white;direction:ltr;unicode-bidi:embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='margin-bottom:0cm;margin-bottom:.0001pt;
+
text-align:left;line-height:normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
+
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;
+
tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
+
background:white;direction:ltr;unicode-bidi:embed'><o:p> </o:p><pre dir=LTR style='background:white'><span class=SpellE><span class=GramE><span
+
style='color:#222222'>sbatch</span></span></span><span style='color:#222222'> –o output.txt --wrap 'head -n 20 file.txt'<o:p></o:p></span></pre><pre
+
dir=LTR style='text-indent:18.0pt;background:white'><span style='color:#222222'><o:p> </o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='font-size:11.0pt;font-family:
+
"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
+
Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;
+
mso-bidi-font-family:Arial;mso-bidi-theme-font:minor-bidi'>The above code will submit the command 'head -n 20 file.txt' as a job to <span
+
class=SpellE>slurm</span> and will write the output of the command (the first 20 lines of ''file.txt'') to the file ''output.txt''. <o:p></o:p></span></pre><p class=MsoNormal dir=LTR style='margin-left:90.0pt;text-align:left;
+
direction:ltr;unicode-bidi:embed'><o:p> </o:p><p class=MsoListParagraph dir=LTR style='margin-top:0cm;margin-right:0cm;
+
margin-bottom:8.0pt;margin-left:36.0pt;mso-add-space:auto;text-align:left;
+
text-indent:-18.0pt;mso-list:l0 level1 lfo1;direction:ltr;unicode-bidi:embed'><![if !supportLists]><span
+
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
+
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>      
+
</span></span></span><![endif]><span dir=LTR></span><span class=SpellE>sbatch</span>
+
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 <span class=SpellE>sbatch</span>
+
argument, and will be parsed by <span class=SpellE>sbatch</span> until the
+
script starts, so <span class=GramE>an</span> #SBATCH argument written after
+
the first command of the script will be ignored by <span class=SpellE>sbatch</span>.
+
Here is an example of a bash script called ''my-sbatch-script.sh'' with <span
+
class=SpellE>sbatch</span> arguments:<pre dir=LTR style='background:white'><span class=GramE><span style='color:
+
#222222'>#!/</span></span><span style='color:#222222'>bin/bash<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH --mem 10GB<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span class=GramE><span style='color:#222222'>echo</span></span><span
+
style='color:#222222'> "hello world" <o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'># <span
+
class=GramE>The</span> following line will not be parsed by <span class=SpellE>sbatch</span><o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH --time 10<o:p></o:p></span></pre><p class=MsoNormal dir=LTR style='margin-left:90.0pt;text-align:left;
+
direction:ltr;unicode-bidi:embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>The above script can then be submitted to the <span class=SpellE>slurm</span>
+
queue from the command line as follows:<pre dir=LTR style='background:white'><span class=SpellE><span class=GramE><span
+
style='color:#222222'>sbatch</span></span></span><span style='color:#222222'> my-sbatch-script.sh<o:p></o:p></span></pre><p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
+
direction:ltr;unicode-bidi:embed'>''<o:p> </o:p>''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span class=GramE>''my-sbatch-script.sh''</span> will be submitted as
+
a job to the <span class=SpellE>slurm</span> 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 <span class=SpellE>sbatch</span> 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><o:p><span style='text-decoration:none'> </span></o:p></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;mso-add-space:auto;text-align:left;
+
text-indent:-18.0pt;mso-list:l1 level1 lfo2;direction:ltr;unicode-bidi:embed'><![if !supportLists]><span
+
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
+
style='mso-list:Ignore'>1-<span style='font:7.0pt "Times New Roman"'>     
+
</span></span></span><![endif]><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;mso-add-space:auto;text-align:left;
+
text-indent:-18.0pt;mso-list:l1 level1 lfo2;direction:ltr;unicode-bidi:embed'><![if !supportLists]><span
+
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
+
style='mso-list:Ignore'>2-<span style='font:7.0pt "Times New Roman"'>     
+
</span></span></span><![endif]><span dir=LTR></span><span
+
style='mso-spacerun:yes'></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:<o:p></o:p>'''<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;mso-add-space:auto;text-align:left;
+
text-indent:-18.0pt;mso-list:l2 level1 lfo3;direction:ltr;unicode-bidi:embed'><![if !supportLists]><span
+
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
+
style='mso-list:Ignore'>1-<span style='font:7.0pt "Times New Roman"'>     
+
</span></span></span><![endif]><span dir=LTR></span>using <span class=SpellE>mpirun</span><p class=MsoListParagraphCxSpMiddle dir=LTR style='margin-top:0cm;margin-right:
+
0cm;margin-bottom:8.0pt;margin-left:36.0pt;mso-add-space:auto;text-align:left;
+
text-indent:-18.0pt;mso-list:l2 level1 lfo3;direction:ltr;unicode-bidi:embed'><![if !supportLists]><span
+
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
+
style='mso-list:Ignore'>2-<span style='font:7.0pt "Times New Roman"'>     
+
</span></span></span><![endif]><span dir=LTR></span>using <span class=SpellE>srun</span><p class=MsoListParagraphCxSpLast dir=LTR style='margin-top:0cm;margin-right:
+
0cm;margin-bottom:8.0pt;margin-left:36.0pt;mso-add-space:auto;text-align:left;
+
text-indent:-18.0pt;mso-list:l2 level1 lfo3;direction:ltr;unicode-bidi:embed'><![if !supportLists]><span
+
style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span
+
style='mso-list:Ignore'>3-<span style='font:7.0pt "Times New Roman"'>     
+
</span></span></span><![endif]><span dir=LTR></span>using an outer submit
+
script – this is recommended as it is the simplest method<span
+
style='mso-spacerun:yes'></span><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>1- <span class=GramE>using</span><span class=SpellE>mpirun</span>:<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 <span
+
class=SpellE>OpenMPI</span>, you can use <span class=SpellE>mpirun</span> to
+
run the program on multiple nodes in parallel – see the <a
+
href="https://www.mpi-forum.org/docs/"><span class=SpellE>mpi</span> manual</a>
+
for more information.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>2- <span class=GramE>using</span><span class=SpellE>srun</span>:<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span class=SpellE>Srun</span> can be used within <span class=GramE>an</span><span class=SpellE>sbatch</span> 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 class=GramE><span style='color:
+
#222222'>#!/</span></span><span style='color:#222222'>bin/bash<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH -N 5<o:p></o:p></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";mso-fareast-font-family:
+
"Times New Roman";color:#222222'><o:p> </o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>files</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>=(file0 file1 file2 file3 file4)<o:p></o:p></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";mso-fareast-font-family:
+
"Times New Roman";color:#222222'><o:p> </o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>for</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><span class=SpellE>i</span> in {0..4}<o:p></o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>do</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><span style='mso-tab-count:1'></span><o:p></o:p></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 class=SpellE><span class=GramE><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>srun</span></span></span><span style='font-size:10.0pt;
+
font-family:"Courier New";mso-fareast-font-family:"Times New Roman";color:#222222'> -N
+
1 –o output.$i.txt head –n 20 ${files[$<span class=SpellE>i</span>]} &<o:p></o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>done</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><o:p></o:p></span><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><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 <span class=SpellE>slurm</span> 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<span class=GramE>.{</span>i}.txt''
+
file. If you submit the above script as a job without using the <span
+
class=SpellE>srun</span> command, for example:<pre dir=LTR style='background:white'><span class=GramE><span style='color:
+
#222222'>#!/</span></span><span style='color:#222222'>bin/bash<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH -N 5<o:p></o:p></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";mso-fareast-font-family:
+
"Times New Roman";color:#222222'><o:p> </o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>files</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>=(file0 file1 file2 file3 file4)<o:p></o:p></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";mso-fareast-font-family:
+
"Times New Roman";color:#222222'><o:p> </o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>for</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><span class=SpellE>i</span> in {0..4}<o:p></o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>do</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><o:p></o:p></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 class=GramE><span style='font-size:
+
10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>head</span></span><span style='font-size:10.0pt;font-family:
+
"Courier New";mso-fareast-font-family:"Times New Roman";color:#222222'> –n 20
+
${files[$<span class=SpellE>i</span>]} &<o:p></o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>done</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><o:p></o:p></span><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><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 <span class=GramE>a for</span>
+
loop in a script that submits all of the jobs at once. For example:<pre dir=LTR style='background:white'><span class=GramE><span style='color:
+
#222222'>#!/</span></span><span style='color:#222222'>bin/bash<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'><o:p> </o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>files</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>=(file0 file1 file2 file3 file4)<o:p></o:p></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";mso-fareast-font-family:
+
"Times New Roman";color:#222222'><o:p> </o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>for</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'> file in ${files[*]}<o:p></o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>do</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><o:p></o:p></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 class=SpellE><span class=GramE><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>sbatch</span></span></span><span style='font-size:10.0pt;
+
font-family:"Courier New";mso-fareast-font-family:"Times New Roman";color:#222222'>
+
head.sh $file <o:p></o:p></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 class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>done</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'><o:p></o:p></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";mso-fareast-font-family:
+
"Times New Roman";color:#222222'><o:p> </o:p></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 <span class=GramE>an</span> argument)
+
as an <span class=SpellE>sbatch</span> job. The ''head.sh'' script will
+
contain the <span class=SpellE>sbatch</span> arguments needed to run on one
+
file. For example:<pre dir=LTR style='background:white'><span class=GramE><span style='color:
+
#222222'>#!/</span></span><span style='color:#222222'>bin/bash<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH –o output.txt<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH –N 1<o:p></o:p></span></pre><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>file</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'>=$1 #first argument from outer script<o:p></o:p></span><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span class=GramE><span style='font-size:10.0pt;font-family:"Courier New";
+
mso-fareast-font-family:"Times New Roman";color:#222222'>head</span></span><span
+
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
+
color:#222222'> –n 20 $file<o:p></o:p></span><p class=MsoNoSpacing dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><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
+
<span class=SpellE>sbatch</span> 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'><span style='mso-spacerun:yes'></span>'''Requesting multiple <span
+
class=SpellE>cpus</span>:<o:p></o:p>'''<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 <span class=SpellE>cpus</span> (up to the maximum) and then
+
run the program while specifying the number of <span class=SpellE>cpus</span>
+
you want it to use as a parameter. For example:<pre dir=LTR style='background:white'><span class=GramE><span style='color:
+
#222222'>#!/</span></span><span style='color:#222222'>bin/bash<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>#SBATCH –c 32 #request 32 <span
+
class=SpellE>cpus</span><o:p></o:p></span></pre><pre dir=LTR style='background:
+
white'><span style='color:#222222'>#SBATCH –o output.txt<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span class=GramE><span style='color:#222222'>sample</span></span><span
+
style='color:#222222'>=$1<o:p></o:p></span></pre><pre dir=LTR style='background:
+
white'><span style='color:#222222'>bowtie2 -p 32 -x $genome -U $sample -S $<span
+
class=SpellE>sam</span> >& bowtie2.log<o:p></o:p></span></pre><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><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 <span class=SpellE>cpus</span> 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'>'''<o:p> </o:p>'''<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>'''Requesting memory:<o:p></o:p>'''<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 <span class=GramE>an</span><span class=SpellE>sbatch</span> job is running you can check its accounting
+
information with the '<span class=SpellE>sacct</span>' 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 <span class=SpellE>slurm</span>
+
wiki</a>.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><u>FAQs <o:p></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>1.<span style='mso-spacerun:yes'></span>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 '<span class=SpellE>squeue</span> –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"><span
+
class=SpellE>squeue</span> manual</a>.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>2.<span style='mso-spacerun:yes'></span>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 '<span class=SpellE>scancel</span><span class=SpellE>jobid</span>' where the <span class=SpellE>jobid</span> is
+
the number that <span class=SpellE>slurm</span> assigned your job when it was
+
submitted which you can see by running '<span class=SpellE>squeue</span> –u
+
username' and looking at the JOBID column.<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>3.<span style='mso-spacerun:yes'></span>Why is my job taking so long
+
to start running?<u><o:p></o:p></u><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>Jobs are prioritized in the <span class=SpellE>slurm</span> 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:
+
embed'>4.<span style='mso-spacerun:yes'></span>How much memory/<span
+
class=SpellE>cpus</span> did my job actually use? <p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>When a job is running, you can use the following commands to see its
+
accounting information:<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span class=SpellE><span class=GramE>sacct</span></span> – see the <a
+
href="https://slurm.schedmd.com/sacct.html"><span class=SpellE>sacct</span>
+
manual</a> for more details<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span class=SpellE><span class=GramE>sstat</span></span> – see the <a
+
href="https://slurm.schedmd.com/sstat.html"><span class=SpellE>sstat</span>
+
manual</a> for more details<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'>5.<span style='mso-spacerun:yes'></span>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:
+
embed'>You can tell a job what time you want it to start running with the
+
parameter --begin:<pre dir=LTR style='background:white'><span style='color:#222222'>#SBATCH --begin HH:MM MM/DD/YY<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'><o:p> </o:p></span></pre><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><span style='mso-spacerun:yes'></span>Alternatively, you can add
+
dependencies to your jobs so that, for example, job #2 will not start until job
+
#1 satisfies the provided condition, by using the job id. This can be done in a
+
bash script:<pre dir=LTR style='background:white'><span class=GramE><span style='color:
+
#222222'>#!/</span></span><span style='color:#222222'>bin/bash<o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='color:#222222'>jobid1=$(<span
+
class=SpellE>sbatch</span> job1.sh)<span style='mso-tab-count:1'></span><o:p></o:p></span></pre><pre
+
dir=LTR style='background:white'><span class=SpellE><span class=GramE><span
+
style='color:#222222'>sbatch</span></span></span><span style='color:#222222'> –-dependency afterok:jobid1 job2.sh<span
+
style='mso-tab-count:1'></span><o:p></o:p></span></pre><pre dir=LTR
+
style='background:white'><span style='color:#222222'><o:p> </o:p></span></pre><pre
+
dir=LTR style='background:white'><span style='font-size:11.0pt;font-family:
+
"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
+
Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;
+
mso-bidi-font-family:Arial;mso-bidi-theme-font:minor-bidi'>The above script submits ''job1.sh'' as a job and saves <span
+
class=SpellE>jobid</span> 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 '<span
+
class=SpellE>afterok</span>'. For more information on possible conditions, <span
+
class=SpellE>etc</span>… please refer to the </span><a
+
href="https://slurm.schedmd.com/sbatch.html"><span class=SpellE><span
+
style='font-size:11.0pt;font-family:"Calibri",sans-serif;mso-ascii-theme-font:
+
minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
+
mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Arial;mso-bidi-theme-font:
+
minor-bidi'>sbatch</span></span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;
+
mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
+
minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Arial;
+
mso-bidi-theme-font:minor-bidi'> manual</span></a><span style='font-size:11.0pt;
+
font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
+
Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;
+
mso-bidi-font-family:Arial;mso-bidi-theme-font:minor-bidi'>.<o:p></o:p></span></pre><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p><p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
+
embed'><o:p> </o:p></div></body></html>
+

Latest revision as of 08:24, 9 July 2018