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
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module load schrodinger/2022-4 |
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find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2022-4/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t autots diagnost gfxinfo jsc material phase_fq qikprop ska biolumin elements glide jws mxmd phase_hy qiksim ssp blast epik HPC1.0Or knime oned_scr phase_qs qpld sta bmin epikx hppmap licadmin Original phase_sc qsite structur confgen fep_abso ifd ligand_s para_tes pipeline run testapp confgenx fep_plus ifd-md ligprep pfam prime schrodin version. consensu fep_solu impact machid phase_bu prime_mm shape_sc vsw constant ffb_fep_ installa macromod phase_da primex shape_sc watermap covalent ffbuilde jaguar maestro phase_fi qikfit sitemap wscore desmond generate jobcontr |
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 hi-core parallel partition for the number of cores specified by the number at the end of its name.
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Host | Partition | Cores being allocated to job |
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slurm-single | general | 24 |
Example Application Usage
qsite
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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 |
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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
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testapp -HOST slurm-parallel-24 -DEBUG para_testapp -HOST slurm-parallel-48 -DEBUG |
Installation Oddities
Schrödinger 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:
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plm_slurm_args = --cpu_bind=boards |
Quantum Espresso
Quantum Espresso can be used to run various Schrödinger suites.
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