Difference between revisions of "Brems"

Latest revision as of 17:56, 1 June 2011

See Running With Slurm for information on running brems.

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-==Brems==
+See [[Running With Slurm]] for information on running brems.
-===Specfications===
-Brems is made of 21 nodes and 60 CPU cores.
-*12 nodes have two 2.0 GHz Opteron CPUs, 2 GB of ECC RAM, and a 40 GB hard drive
-*9 nodes have two dual-core 2.0 GHz Opteron CPUs, 4 GB of ECC RAM, and a 80 GB hard drive
-*The head node also has 1.75 TB of redundant RAID5 storage.
-==Running on Brems==
-===MPI===
-===Querying Brems usage===
-This is a typical output from the command cps2
-<pre>
-brian@brems:~$ cps2
-************************* brems *************************
---------- brems1---------
-pctcpu: 26.00    fname: process.pl    time: 260000    uname: brian
-pctcpu: 2.50    fname: python    time: 50000    uname: brian
-pctcpu: 1.00    fname: ssh    time: 20000    uname: brian
---------- brems2---------
-pctcpu: inf    fname: process.pl    time: 210000    uname: brian
-pctcpu: 1.31    fname: mcnpx-mpi-e2    time: 16761650000    uname: makavakh
-pctcpu: 1.08    fname: mcnpx-mpi-e2    time: 25739210000    uname: makavakh
---------- brems3---------
-pctcpu: 23.00    fname: process.pl    time: 230000    uname: brian
-pctcpu: 0.01    fname: rpciod/1    time: 517950000    uname: root
-pctcpu: 0.00    fname: sshd    time: 0    uname: brian
-...
---------- brems21---------
-pctcpu: 20.00    fname: process.pl    time: 200000    uname: brian
-pctcpu: 0.00    fname: sshd    time: 0    uname: brian
-pctcpu: 0.00    fname: sshd    time: 0    uname: root
-pctcpu: 0.00    fname: lockd    time: 0    uname: root
-pctcpu: 0.00    fname: rpciod/3    time: 20000    uname: root
-pctcpu: 0.00    fname: rpciod/2    time: 0    uname: root
-</pre>
-The cps2 command shows all the processes taking up CPU time on all the cluster nodes. If someone is already running, you will see output similar to the following:
-<pre>
-Paste busy cps2 here
-</pre>
-===Screen===
-Screen is currently the preferred way to run processes on Brems. It allows you to run programs in such a way that they won't terminate when you log off, and you can control the application and see the output in real time.
-====Basic screen usage====
-*Use screen -R to connect a screen session, or start a new one if none exist.
-*Ctrl-a disconnects from within a screen session
-=====Examples=====
-Start a screen session:
-<pre>
-brian@brems:~$ screen -R
-</pre>
-Do some work in the screen session:
-<pre>
-brian@brems:~/work$ /brems/bin/mpirun -np 4 /brems/bin/mcnpx-mpi-e2 i=test1.i
- mcnpx    ver=2.5e  ld=Mon Feb 23 09:00:00 MST 2004   06/26/08 15:34:56
- *****************************************************
- *                                                   *
- *            Copyright Notice for MCNPX             *
-</pre>
-Hitting Ctrl-a disconnects from the screen, and ps shows MCNPX still running:
-<pre>
-brian@brems:~$ screen -R
-[detached]
-brian@brems:~$ ps ux | grep mcnpx
-brian    30339  0.5  0.0   9132  1844 pts/10   S+   15:40   0:00 /bin/sh /brems/bin/mpirun -np 4 /brems/bin/mcnpx-mpi-e2 i=test1.i
-brian    30467  9.5  0.4  43300  9400 pts/10   S+   15:40   0:00 /brems/bin/mcnpx-mpi-e2 i=test1.i -p4pg /home/brian/work/PI30339 -p4wd /home/brian/work
-brian    30468  0.0  0.0  21476   544 pts/10   S+   15:40   0:00 /brems/bin/mcnpx-mpi-e2 i=test1.i -p4pg /home/brian/work/PI30339 -p4wd /home/brian/work
-brian    30469  0.3  0.1  21344  2380 pts/10   S+   15:40   0:00 /usr/bin/rsh brems2 -l brian -n /brems/bin/mcnpx-mpi-e2 brems.iac.isu.edu 45735 \-p4amslave \-p4yourname brems2 \-p4rmrank 1
-brian    30470  0.0  0.1  21340  2376 pts/10   S+   15:40   0:00 /usr/bin/rsh brems3 -l brian -n /brems/bin/mcnpx-mpi-e2 brems.iac.isu.edu 45735 \-p4amslave \-p4yourname brems3 \-p4rmrank 2
-brian    30471  0.3  0.1  21340  2376 pts/10   S+   15:40   0:00 /usr/bin/rsh brems4 -l brian -n /brems/bin/mcnpx-mpi-e2 brems.iac.isu.edu 45735 \-p4amslave \-p4yourname brems4 \-p4rmrank 3
-brian    30473  0.0  0.0   4372   656 pts/0    S+   15:40   0:00 grep mcnpx
-http://www.hpcwire.com/topic/processors/GPGPUs_Make_Headway_in_Bioscience.html
-</pre>
-And we can connect back to the screen session to see the MCNPX output:
-<pre>
-brian@brems:~$ screen -R
-</pre>
-<pre>
- run terminated when    100000 particle histories were done.
- warning.  tally  11 tfc bin did not pass  1 of 10 statistical checks.
- warning.     1 of   7 tallies did not pass all 10 statistical checks.
- warning.     2 of   7 tallies had bins with large relative errors.
- dump   11 on file runtpr     nps =      100000  coll =       31827944
-                              ctm =      3.75     nrn =      514286097
- mcrun  is done
-FORTRAN STOP
-FORTRAN STOP
-FORTRAN STOP
-FORTRAN STOP
-brian@brems:~/work$
-</pre>
-====Advanced screen tricks====
-*Using screen without -r or -R allows you to start a new screen session even if one already exists
-*Using screen -list shows you the current screen sessions you have
-<pre>
-brian@brems:~$ screen
-[detached]
-brian@brems:~$ screen -list
-There are screens on:
-.pts-0.brems	(Detached)
-.pts-0.brems	(Detached)
-Sockets in /var/run/screen/S-brian.
-brian@brems:~$
-</pre>
-You can choose which one to reattach to by specifying a unique part of the name:
-<pre>
-brian@brems:~$ screen -r 298
-</pre>
-===MCNPX===
-==Compiling on Brems==
-===gcc===
-===Portland Group===

Difference between revisions of "Brems"

Latest revision as of 17:56, 1 June 2011

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