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Computational chemistry packages (efficient usage issues?)

Computational chemistry packages (efficient usage issues?). Jemmy Hu SHARCNET HPC Consultant Summer School June 3, 2016. /work/jemmyhu/ss2016/chemistry/. Chemistry Software managed by SHARCNET. User/group owned software (commercial). Nature of the software. General policy for software.

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Computational chemistry packages (efficient usage issues?)

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  1. Computational chemistry packages(efficient usage issues?) Jemmy Hu SHARCNET HPC Consultant Summer School June 3, 2016 /work/jemmyhu/ss2016/chemistry/

  2. Chemistry Software managed by SHARCNET User/group owned software (commercial)

  3. Nature of the software

  4. General policy for software • Open Software used by 2 or more groups– add to SHARCNET software stack with software usage instruction/example webpage online https://www.sharcnet.ca/my/software • Software used by one group – user installs in his/her own space with help from SHARCNET if necessary • SHARCNET owned commercial software – free • Self owned software – user’s response for license issues • Software are installed as module package, setup in your bash configuration file, i.e., .bash_profile file under /home/userid/ module load gaussian/g09_D.01

  5. module load packages • Login to a cluster, e.g., ssh userID@saw.sharcnet.ca • Open the shell configuration file, e.g., vi .bash_profile • Add the module load lines at the end of the file module load gaussian/g09_D.01 module load adf/2014.05 module load nwchem/6.5 module load espresso/5.1.1 module load orca/3.0 • Save the file • Exit • Re-login • Goto your /work directory: cd /work/userID • Copy the files cp –rf /work/jemmyhu/ss2016/chemistry .

  6. System Info Parallel Computer Memory Architectures Hybrid Distributed-Shared Memory (Cluster solution)

  7. Size of Threaded Jobs on specific system https://www.sharcnet.ca/my/systems Job usesless than the max threads and memory on a node will be preferable

  8. Gaussian 09 issues • Latest version: g09-D.01 • Input sample • File location • Memory • Disk • Restart • Utilities https://www.sharcnet.ca/my/software/show/21

  9. G09 input file: simplest case #p b3lyp/6-311++g(2df,p) opt freq << CO-6311++g(2df,p)—B3LYP-Opt-Freq >> 0 1 c o 1 co co=1.1281 (leave an blank line at the end) File name: CO-b3lyp-1.com

  10. Run job, file structure • Real jobs should be submitted to the threaded queue using sqsub command • First check the files under your /work and /scratch directory open two windows, one for /work, one to view files in /scratch • For testing purpose today, we run jobs from command line on the dev. node on saw (saw-dev1, …, saw-dev6) ssh saw-dev4 • run g09 CO-b3lyp-1.com >& CO-b3lyp-1.log & • Output file CO-b3lyp-1.log • Runtime files (5 of them, .rwf is big) /scratch/userID • Job uses defaults [1 cpu, minimum memory (256MB?)] • Only .log output file will be generated in the run directory • Runtime files will be removed automatically once finished successfully, otherwise they will stay.

  11. Specify checkpoint file: name.chk %chk=CO-b3lyp-1chk#p b3lyp/6-311++g(2df,p) opt freq << CO-6311++g(2df,p)—B3LYP-Opt-Freq >> 0 1 c o 1 co co=1.1281 Input file: CO-b3lyp-1chk.com Run on dev: g09 CO-b3lyp-1chk.com >& CO-b3lyp-1chk.log & Files: CO-b3lyp-1chk.log, CO-b3lyp-1chk.chk

  12. G09 input file: CO-b3lyp-4.com, use 4 cpus %nosave%mem=500MB%chk=CO-b3lyp-4%nproc=4#p b3lyp/6-311++g(2df,p) opt freq << CO-6311++g(2df,p)—B3LYP-Opt-Freq >> 0 1 c o 1 co co=1.1281

  13. Run Job in the queue %mem=500MB (--mpp=2x%mem, memory per job, for all cpus)%nproc=4 (-n 4) Submit command issqsub -q threaded -n 4 -r 1.0d –mpp=2g -o CO-6311-4.out g09 CO-6311-4.com What’s happening afterwards? • sqjobs to see job status, jobID • If runs, where are the files? .log and .chk files are generated in the run directory runtime files, .rwf, etc will be in /scratch/yourID/jobID/ • Failed? remove the runtime files, rm –rf /scratch/yourID/jobID . correct input file, re-run

  14. Input file with named .rwf: CO-b3lyp-4rwf.com %rwf=CO-b3lyp-4rwf %nosave%mem=500MB%chk=CO-b3lyp-4rwf%nproc=4#p b3lyp/6-311++g(2df,p) opt freq << CO-6311++g(2df,p)—B3LYP-Opt-Freq >> 0 1 c o 1 co co=1.1281 The named .rwf file will be generated in the current directory

  15. Checkpointing • .chk can be used to restart an Optimization job, or used for • property (freq, etc) calculation afterwards. • 2. In G09, .rwf can be used to restart a frequency calculation.

  16. Restart (see examples) %NoSave %chk=Cu_test.chk %mem=500mb %nproc=4 #B3LYP/DGDZVP Opt Geom=AllCheck Guess=Read (one blank line) • Restart opt job from .chk • Restart freq from .rwf %rwf=/scratch/jemmyhu/Cu_test.rwf %NoSave %chk=Cu_test.chk %mem=500mb %nproc=4 #p restart (one blank line)

  17. Gaussian Utilities • Utilities formchk cubegen freqchk …… use the same version direct run from command line • NBO

  18. Review • Input file, memory (%mem) /cpu (%nproc) • sqsub (-n, --mpp) , sqjobs, sqkill • Use job info from scheduler • File location • Failed jobs • File cleanup

  19. ADF • ADF is frequently used for studying transition metal complexes and molecules with heavy atoms. ADF offers unique capabilities to predict molecular properties of organic electronics materials. • ADF, BAND, DFTB • https://www.scm.com/

  20. Use ADF on SHARCNET • Available on major clusters, viz-stations • Versions: 2013.01, 2014.05 • Setup, add module load line to .bash_profile file, i.e., module load adf/2014.05 • Examples /opt/sharcnet/adf/2014.05/examples

  21. Default settings [jemmyhu@saw-login1:~/tests/test_ADF/saw/test_adf] module show adf/2014.05 ------------------------------------------------------------------- /opt/sharcnet/modules/adf/2014.05: module-whatis Provides ADF 2014.05 binary for x86_64 Centos 6 systems conflict adf setenv ADFROOT /opt/sharcnet/adf setenv ADFHOME /opt/sharcnet/adf/2014.05 setenv ADFBIN /opt/sharcnet/adf/2014.05/bin setenv ADFRESOURCES /opt/sharcnet/adf/2014.05/atomicdata setenv SCMLICENSE /opt/sharcnet/adf/2014.05/license setenv SCM_TMPDIR /scratch/jemmyhu setenv SCM_USETMPDIR yes prepend-path PATH /opt/sharcnet/adf/2014.05/bin -------------------------------------------------------------------

  22. Two input options https://www.sharcnet.ca/help/index.php/ADF/BAND • name.inp (one step a time) use a runscript ‘ADF’ or ‘BAND’, to bypass the runtime files to /scratch/username/jobid/ sqsub -q mpi --nompirun -n 8 --mpp=2g -r 1.0d -o GO_H2O-adf.log ADF GO_H2O-adf.inp sqsub -q mpi --nompirun -n 8 --ppn=4 --mpp=2g -r 1.0d -o GO_H2O-adf.log ADF GO_H2O-adf.inp sqsub -q mpi --nompirun -n 8 --mpp=2g -r 1.0d -o name_band.log BAND name_band.inp

  23. /home/jemmyhu/work/ss2016/chemistry/examples/adf GO_H2O-adf.inp

  24. Input for multi-steps: name.run sqsub -q mpi --nompirun -n 8 --ppn=4 --mpp=2g -r 1.0d -o NMR_B3LYP.log ./NMR_B3LYP.run runtime files are under /scratch/username/

  25. Restart • TAPE13 It serves as a checkpoint file. TAPE13 can be used to restart the calculation at a point not too far before the fatal condition occurred TAPE13 is upgraded during the calculation but discarded upon normal termination. To keep TAPE13, -use the SAVE key • TAPE21 Upon normal (i.e. program-controlled) termination of a calculation, the TAPE21 result file can be used for restart purposes When a crash occurs, however, chances are that TAPE21 has not correctly been closed and that its data structure is inconsistent

  26. ADF GUI • GUI software to run on viz-workstations vdi-centos6.user.sharcnet.ca viz-uwo10.sharcnet.ca viz-uwo11.sharcnet.ca • Turn on X11 locally, then login to he workstation • adfview

  27. https://www.sharcnet.ca/help/index.php/NWCHEM

  28. RUN nwchem on SHARCNET [jemmyhu@saw333:~/work/ss2016/chemistry/examples/nwchem] pwd /home/jemmyhu/work/ss2016/chemistry/examples/nwchem [jemmyhu@saw333:~/work/ss2016/chemistry/examples/nwchem] ls h2o_hu.nw sqsub -q mpi -n 4 -r 3.0d --mpp=4g -o h2o_hu.log nwchem h2o_hu.nw

  29. https://www.sharcnet.ca/help/index.php/ESPRESSO

  30. https://www.sharcnet.ca/help/index.php/ORCA

  31. Research group owns the license Installation guideline https://www.sharcnet.ca/help/index.php/VASP

  32. What else? • Question? • Discussion?

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