Difference between revisions of "Schrödinger Guide"

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(Added section describing an oddity with the mpi setup in schrodinger)
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$ find /apps2/schrodinger/2016-2 -maxdepth 1 -executable -type f -printf "%f\n" | sort | column
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$ find /apps2/schrodinger/2016-2 -maxdepth 1 -executable -type f -printf "%f\n" | sort | column -t
blast epik jobcontrol mcpro_fep phase_inactive primex sta
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blast               epik               jobcontrol     mcpro_fep             phase_inactive       primex       sta
bmin fep_plus knime mcpro_lrm phase_multiPartition qikfit strike
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bmin               fep_plus           knime         mcpro_lrm             phase_multiPartition qikfit       strike
canvas gfxinfo licadmin membrane_permeability phase_multiQsar qikprop structurebased_adme
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canvas             gfxinfo             licadmin       membrane_permeability phase_multiQsar       qikprop       structurebased_adme
combgen glide ligand_strain para_testapp phase_partition qiksim testapp
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combgen             glide               ligand_strain para_testapp           phase_partition       qiksim       testapp
combiglide hppmap ligprep pfam phase_qsar qpld vsw
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combiglide         hppmap             ligprep       pfam                   phase_qsar           qpld         vsw
confgen hunt lsbd phase_build_qsar phase_scoring qsite
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confgen             hunt               lsbd           phase_build_qsar       phase_scoring         qsite
confgenx ifd machid phase_database phase_screen run
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confgenx           ifd                 machid         phase_database         phase_screen         run
consensus_homology impact macromodel phase_feature pipeline shape_screen
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consensus_homology impact             macromodel     phase_feature         pipeline             shape_screen
covalent_docking installation_check maestro phase_find_common platform sitemap
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covalent_docking   installation_check maestro       phase_find_common     platform             sitemap
desmond jagscript mcpro phase_fqsar prime ska
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desmond             jagscript           mcpro         phase_fqsar           prime                 ska
diagnostics jaguar mcpro_ddg phase_hypoCluster prime_mmgbsa sip
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diagnostics         jaguar             mcpro_ddg     phase_hypoCluster     prime_mmgbsa         sip
 
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Revision as of 14:15, 5 June 2019

The Schrödinger Suite is a collection of software for chemical and biochemical use. It offers various tools that facilitate the investigation of the structures, reactivity and properties of chemical systems. There is a campus site license for this software, supported by UITS. More information is available here: http://software.uconn.edu/schrodinger/.

Load Modules

$ module load schrodinger/2016-2

You can then see a list of executable programs:

$ find /apps2/schrodinger/2016-2 -maxdepth 1 -executable -type f -printf "%f\n" | sort | column -t
blast               epik                jobcontrol     mcpro_fep              phase_inactive        primex        sta
bmin                fep_plus            knime          mcpro_lrm              phase_multiPartition  qikfit        strike
canvas              gfxinfo             licadmin       membrane_permeability  phase_multiQsar       qikprop       structurebased_adme
combgen             glide               ligand_strain  para_testapp           phase_partition       qiksim        testapp
combiglide          hppmap              ligprep        pfam                   phase_qsar            qpld          vsw
confgen             hunt                lsbd           phase_build_qsar       phase_scoring         qsite
confgenx            ifd                 machid         phase_database         phase_screen          run
consensus_homology  impact              macromodel     phase_feature          pipeline              shape_screen
covalent_docking    installation_check  maestro        phase_find_common      platform              sitemap
desmond             jagscript           mcpro          phase_fqsar            prime                 ska
diagnostics         jaguar              mcpro_ddg      phase_hypoCluster      prime_mmgbsa          sip

Host Configuration

The Schrödinger Suite is configured to submit jobs directly to the SLURM job scheduler. Therefore, you do not need to wrap your commands in a submission script. You can execute Schrödinger commands directly from a login node. When you submit Schrödinger jobs, you do so to hosts. We have created the following hosts: slurm-parallel-24, slurm-parallel-48, slurm-parallel-96, slurm-parallel-192, slurm-parallel-384. Each one of these hosts will submit a job to SLURM's parallel for the number of cores specified by the number at the end of its name.

Example Application Usage

qsite

$ qsite -SAVE -PARALLEL 24 -HOST slurm-parallel-24 3IIS_Per1.in 
Launching JAGUAR under jobcontrol.
Exec: /apps2/schrodinger/2016-2/jaguar-v9.2/bin/Linux-x86_64
JobId: cn01-0-57b33646

Note that the numeric value of -PARALLEL should match the numeric value of the -HOST that you specified.

You can then view the status of your running job with sacct.

$ sacct
       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode 
------------ ---------- ---------- ---------- ---------- ---------- -------- 
39148       j3IIS_Per1   parallel   abc12345         24    RUNNING      0:0 
391148.0       hostname              abc12345         24  COMPLETED      0:0

Run Test Suite

$ testapp -HOST slurm-parallel-24 -DEBUG
$ para_testapp -HOST slurm-parallel-48 -DEBUG

Installation Oddities

schrodinger comes pre-packaged with an outdated version of mpi(< 1.8.1), meaning an old bug in the MPI->SLURM interface needs to be manually patched by appending the following line to schrodinger's mpi's default config file:

plm_slurm_args = --cpu_bind=boards

This causes cpu affinities to be set sub-optimally, but better than how they are set without the cpu_bind line. To append this line to the 2016-3 install an admin would do:

echo 'plm_slurm_args = --cpu_bind=boards' >> /apps2/schrodinger/2017-1/mmshare-v3.7/lib/Linux-x86_64/openmpi/etc/openmpi-mca-params.conf