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/ .
It is recommended currently to use Schrodinger through an interactive session because of some issues encountered when submitting jobs through submission scripts.
Start an interactive session:
srun --x11 -N 1 -n 126 -p general --constraint=epyc128 --pty bash
Make sure to include the “--x11” flag for the GUI
Load Modules
module load schrodinger/2023-3
You can then see a list of executable programs:
find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2023-3/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t autots elements hppmap knime mxmd phase_qs qpld ska biolumin epik ifd lambda_d oned_scr phase_sc qsite ssp blast epikx ifd-md licadmin para_tes pipeline quick_sh sta bmin fep_abso impact ligand_s pfam prime run structur confgen fep_plus installa ligprep phase_bu prime_mm schrodin testapp confgenx fep_solu jaguar machid phase_da primex shape_sc vsw consensu ffbuilde jobcontr macromod phase_fi qikfit shape_sc watermap constant generate jsc maestro phase_fq qikprop shape_sc wscore covalent gfxinfo jws material phase_hy qiksim sitemap xtb desmond glide
You can also see a list of utilities with the same find command above:
find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2023-3/utilities/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t 2d_sketc canvasHC cg_chsr create_w jaguar_p mtzprint project_ structal abs canvasHC check_jo create_x jaguar_t multisim project_ structca align_bi canvasKM check_re create_x jaguar_t neutrali project_ structco align_hy canvasKP check_th create_x jnanny numfreqc propfilt structsh align_li canvasLC ch_isost custom_p jobcontr obabel proplist structsu anharmon canvasLi ch_ligan desalter jresults para_bmi protassi structur apbs canvas_m ch_water elim.sch jserver para_epi py.test stu_add applyhtr canvasMC cluster_ epharmac jserver_ para_lig query_gp stu_dele autoqsar canvasMD combinat extract_ lictest path_fin queue_bm stu_exec AutoTSRe canvasML combinat feature_ licutil pbs_lic_ randsub stu_extr AutoTSRe canvasMo combinat feature_ ligand_i pdbconve refconve stu_modi AutoTSRe canvasNn combinat ffld_ser ligfilte phase_al render_k stu_work AutoTSUn canvasPC compare_ flex_ali ligparse phase_cl r_group_ system_b babel canvasPC configur flexlm_s lp_filte phase_co r_group_ tautomer bandshap canvasPC conf_tem fragment lp_label phase_co ring_con thermoch buildloo canvasPC convert_ generate lp_nored phase_de ring_tem timestam canvasBa canvasPh convert_ generate macro_pk phase_hy rmsdcalc uffmin canvasCo canvasPL convert_ getpdb maegears phase_hy rsync_pd unique_n canvasCS canvasPr convert_ glide_en maetopqr phase_hy sdconver uniquesm canvasCS canvasPW corefind glide_me mae_to_s phase_mm secstruc update_B canvasCS canvasRP create_h glide_so make_lin phase_pr seqconve update_P canvasDB canvasSc create_h guardian make_r_l phase_qs serial_s vis2gc canvasFP canvasSD create_h hetgrp_f md5diges phase_vo shape_sc visdump canvasFP canvasSe create_h hit_expa merge_du postmort show_joi watermap canvasFP canvasSO create_i impref micro_pk premin smiles_t wscore_m canvasFP canvasSO create_m ionizer modify_s prepwiza spectrum wscore_r canvasFP canvasTr create_r ionizer_ mol2conv profile_ stereoiz zip_temp canvasHC ccp42cns create_s jagconve moldescr profile_ store_re ziputil
Example Application Usage
qsite
qsite -SAVE -PARALLEL 24 -HOST slurm-parallel-24 3IIS_Per1.in Launching JAGUAR under jobcontrol. Exec: /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/2022-4/jaguar-v11.8/bin/Linux-x86_64 JobId: job60-login5-1674022
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 hi-core 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
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:
plm_slurm_args = --cpu_bind=boards
Command to call a Schrodinger utility
"${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_md_job_TREK1model_1ms < restOfCommandOptions >
Example Submission Script CPU
#!/bin/bash #SBATCH --partition=general # Name of Partition #SBATCH --ntasks=126 # Maximum CPU cores for job #SBATCH --nodes=1 # Ensure all cores are from the same node #SBATCH --mem=492G # Request 128 GB of available RAM #SBATCH --constraint='epyc128' # Request AMD EPYC node for the job #SBATCH --mail-type=END # Event(s) that triggers email notification (BEGIN,END,FAIL,ALL) #SBATCH --mail-user=first.lastname@uconn.edu # Destination email address module load schrodinger/2022-4 <schrodinger program> <other options>
Example Submission Script GPU
#!/bin/bash #SBATCH --partition=general-gpu # Name of Partition #SBATCH --ntasks=20 # Maximum CPU cores for job #SBATCH --nodes=1 # Ensure all cores are from the same node #SBATCH --mem=128G # Request 128 GB of available RAM #SBATCH --gres=gpu:2 # Request 2 GPU cards for the job #SBATCH --mail-type=END # Event(s) that triggers email notification (BEGIN,END,FAIL,ALL) #SBATCH --mail-user=first.lastname@uconn.edu # Destination email address module load schrodinger/2022-4 <schrodinger program> <other options>