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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.

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Week 5 Friday

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  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

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