1 / 12

Week 5 Friday

Tom's Back... mardi gras is over. Week 5 Friday. Today and Beyond. Today: Using LONI Next Week start on TCBG Tutorials in syllabus. LONI. louie.loni.org : Tulane oliver.loni.org : ULL(?) poseidon.loni.org : UNO eric.loni.org : LSU painter.loni.org : LaTech Queenbee.loni.org: Baton Rouge.

azizi
Download Presentation

Week 5 Friday

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Tom's Back... mardi gras is over Week 5 Friday

  2. Today and Beyond • Today: Using LONI • Next Week start on TCBG Tutorials in syllabus

  3. LONI louie.loni.org : Tulane oliver.loni.org : ULL(?) poseidon.loni.org : UNO eric.loni.org : LSU painter.loni.org : LaTech Queenbee.loni.org: Baton Rouge

  4. Secure shell access Windows: winscp or putty http://winscp.net/eng/index.php http://www.putty.org/ Linux: should be there Ssh louie.loni.org Mac: ???

  5. Secure shell keys http://paulkeck.com/ssh/ Allows for access w/out a password ssh-keygen -t dsa scp ~/.ssh/id_dsa.pub burly:.ssh/authorized_keys2 ssh-agent sh -c 'ssh-add < /dev/null && bash' ssh burly

  6. Our LONI Allocation https://allocations.loni.org/balances.php Allocation NAME: loni_lasigma_md USAGE: only for class assignments

  7. Submitting Jobs with PBS Basic PBS info https://docs.loni.org/wiki/Submitting_a_Batch_Job_in_PBS Job Dependencies https://docs.loni.org/wiki/PBS_Job_Chains_and_Dependencies

  8. The New Documentation See http://www.hpc.lsu.edu/docs/guides/index.php

  9. Softenv or not? Man soft: SOFT(1) User Contributed Perl Documentation SOFT(1) NAME soft - dynamically change the environment by adding or deleting keys DESCRIPTION This program dynamically changes your software environment. By specifing either add or delete and specifying a keyword, that keyword will be added or deleted from your environment. NOTE: This manual page only describes basic information for the program titled soft. If you are new to the SoftEnv sys- tem, refer to ’man softenv-intro’. For administration details, refer to ’man softenv-admin’. More detailed information about this program can alo be found in those manual pages.

  10. Queuing a NAMD job Put namd in ~/bin onall “qfree”

  11. Queuing a NAMD job that I created for LONI systems: namd2.qsub namd2.tcsh to run namd one merely needs to setup their files whereever then call namd2.qsub <CONF> < LOG> < NODES> <ALLOCATION> <walltime> <queue> this in turn calls namd2.tcsh change set SYSNAMD = "/home/bishop/bin/NAMD_2.9_Linux-x86_64-ibverbs/" to whatever ya'll want or make it a softenv and you're done! it needs some checks to change the walltime and/or queue from teh default values. NOTE: if you want to use it on other LONI systems then simply set PPN=4 I've used something similar to this on all LONI systems and it seems to work well. Merry Christmas! Tom

  12. Queuing a NAMD job Dear Thomas C. Bishop, It looks like your .soft file is already set up to use the installed NAMD-2.9. Verify you are using the correct namd. Typing "which namd2" should produce: /usr/local/packages/NAMD/2.9/Linux-x86_64-MPI-intel/namd2 Verify you are using openmpi-1.3.4. "which mpirun" should produce: /usr/local/packages/openmpi/1.3.4/intel-11.1/bin/mpirun In your "namd2.qsub" file, remove the "setenv CHARMRUN" and "setenv NAMD" lines. In your "namd2.tcsh", change the "CHARMRUN" execution line to read: mpirun -machinefile $PBS_NODEFILE -np $np namd2 $CONF > $LOG That should do it. This should work on any LONI machine. If you find NAMD-2.9 is missing, let us know and we'll install it, but I check and it appears on all the systems. The current ticket state is: "open" James Lupo

More Related