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/ .
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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:
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srun --x11 -N 1 -n 126 -p general --constraint=epyc128 --pty bash |
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Make sure to include the “--x11” flag for the GUI |
Load Modules
Once a node is assigned to the interactive srun job in the previous section, schrodinger can be loaded from one of the various modules available on HPC.
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module load schrodinger/20222023-43 |
You can then see a list of executable programs:
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find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/20222023-43/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t autots desmond gfxinfo jsc material phase_hy qiksim ska biolumin elements glidehppmap knime jws mxmd phase_qs qpld ssp blast ska biolumin epik hppmapifd knime lambda_d oned_scr phase_sc qsite stassp bminblast epikx ifd -md licadmin para_tes pipeline runquick_sh sta bmin structur confgen fep_abso ifd-mdimpact ligand_s pfam prime run schrodin structur testappconfgen confgenx fep_plus impact installa ligprep phase_bu prime_mm shape_scschrodin vswtestapp consensuconfgenx fep_solu jaguar installa machid phase_da primex shape_sc watermapvsw constantconsensu ffbuilde jaguarjobcontr macromod phase_fi qikfit shape_sc wscorewatermap covalentconstant generate jsc jobcontr 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:
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find /gpfs/sharedfs1/admin/hpc2.0/apps/schrodinger/20222023-43/utilities/ -maxdepth 1 -executable -type f -printf "%f\n" | sort | pr -tT -8 | column -t 2d_sketc canvasHC ccp42cnscg_chsr create_xw jnannyjaguar_p neutralimtzprint project_ store_restructal abs canvasHC cgcheck_chsr jo create_x jobcontrjaguar_t numfreqcmultisim project_ structalstructca align_bi canvasJocanvasKM check_jore create_x jserver obabel jaguar_t neutrali project_ structco align_hy canvasKP check_th create_x jnanny numfreqc propfilt structcastructsh align_hyli canvasKMcanvasLC checkch_thisost custom_p jobcontr jserver_obabel para_bmi proplist structcostructsu align_lianharmon canvasKPcanvasLi ch_isostligan desalter lictest jresults para_epibmi protassi structsh anharmonstructur apbs canvasLCcanvas_m ch_liganwater elim.sch licutiljserver para_ligepi py.test structurstu_add apbsapplyhtr canvasMC canvasLi ch_watercluster_ epharmac ligandjserver_i pathpara_finlig query_gp stu_adddele applyhtrautoqsar canvas_mcanvasMD cluster_combinat extract_ lictest ligfilte pbspath_lic_fin queue_bm stu_deleexec autoqsarAutoTSRe canvasMCcanvasML combinat feature_ licutil ligparse pdbconvepbs_lic_ randsub stu_execextr AutoTSRe canvasMDcanvasMo combinat feature_ lpligand_filtei phase_alpdbconve refconve stu_extrmodi AutoTSRe canvasMLcanvasNn combinat ffld_ser lp_labelligfilte phase_clal render_k stu_modiwork AutoTSReAutoTSUn canvasMocanvasPC combinatcompare_ flex_ali lp_noredligparse phase_cocl r_group_ stusystem_workb babel canvasNncanvasPC compare_configur flexlm_s macrolp_pkfilte phase_co r_group_ system_btautomer bandshap canvasPC configurconf_tem fragment maegearslp_label phase_deco ring_con tautomerthermoch buildloo canvasPC confconvert_tem generate maesubselp_nored phase_hyde ring_tem thermochtimestam canvas_acanvasBa canvasPCcanvasPh convert_ generate maetopqrmacro_pk phase_hy rmsdcalc timestamuffmin canvasBacanvasCo canvasPCcanvasPL convert_ getpdb mae_to_smaegears phase_hy rsync_pd uffminunique_n canvasCocanvasCS canvasPhcanvasPr convert_ glide_en makejbasmaetopqr phase_mmhy sdconver unique_nuniquesm canvasCS canvasPLcanvasPW convert_corefind glide_me makemae_to_lins phase_prmm sdsubsetsecstruc uniquesmupdate_B canvasCS canvasPrcanvasRP corefindcreate_h glide_so make_r_llin phase_qspr secstrucseqconve update_BP canvasCScanvasDB canvasPWcanvasSc create_h guardian md5digesmake_r_l phase_voqs seqconveserial_s vis2gc canvasDBcanvasFP canvasRPcanvasSD create_h hetgrp_f merge_dumd5diges postmortphase_vo serialshape_ssc visdump canvasFP canvasSccanvasSe create_h hit_expa micromerge_pkdu preminpostmort shapeshow_scjoi watermap canvasFP canvasSDcanvasSO create_hi impref micro_pk mol2convpremin prepwiza showsmiles_joit wscore_m canvasFP canvasSecanvasSO create_im ionizer moldescrmodify_s profile_prepwiza smiles_tspectrum wscore_r canvasFP canvasSOcanvasTr create_mr ionizer_ mtzprintmol2conv profile_ spectrumstereoiz zip_temp canvasFPcanvasHC canvasSOccp42cns create_s jagconve multisimmoldescr projectprofile_ stereoizstore_re ziputil canvasHC canvasTr create_w jaguar_p |
Example Application Usage
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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 -HOSTn declaration that you specified in the previous srun command.
Jaguar
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jaguar run nameofinput.in |
There is a way to target a specific Schrodinger application or utility with the following syntax:
You can then view the status of your running job with sacct.
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Run Test Suite
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testapp -HOST slurm-parallel-24 -DEBUG para_testapp -HOST slurm-parallel-48 -DEBUG |
Installation Oddities
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"${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_md_job_TREK1model_1ms < restOfCommandOptions > |
Example Submission Script CPU
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#!/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 |
Launching and disconnecting from an interactive fisbatch Schrodinger job
Schrodinger can be run interactively through srun or fisbatch.
The srun solution above is good for a single interactive calculation that can be left up and running without any disconnections.
If there are network or power interruptions while the Interactive Schrodinger srun job is running, the srun job will end and progress will be lost.
An alternative to avoid potential network/power interruptions for an interactive SLURM srun job would be to submit an interactive fisbatch job to HPC.
Fisbatch is older and it does have some bugs.
Fisbatch allocates a compute node to the job session, which allows users to spawn a calculation interactively through a screen session that launches on the assigned compute node,.
Users can also disconnect from the fisbatch job, and reattach to the job to track the progress of various calculations.
Here is an example to allocate an AMD EPYC compute node with 126 cores through fisbatch under the general partition:
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fisbatch -N 1 -n 126 -p general --constraint='epyc128' FISBATCH -- waiting for JOBID jobidhere to start on cluster=slurm and partition=general .........................! Warning: # 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 Permanently added 'cXX,137.99.x.x' (ECDSA) to the list of known hosts. FISBATCH -- Connecting to head node (cnXX) |
Once a compute node is assigned and the fisbatch job is running, schrodinger can be loaded normally through the module.
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module load schrodinger/2022-4
<schrodinger program> <other options> |
Example Submission Script GPU
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#!/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> 2023-3 |
Once schrodinger is loaded, the Schrodinger commands will become available and the Schrodinger calculations can be called through one of the many Schrodinger suites.
To disconnect from a fisbatch job, enter the following key strokes:
“Ctrl-a then Ctrl-d”
The screen session that fisbatch spawns on the compute node should detach and the fisbatch job will continue running.
To confirm that the job is still running, the following SLURM command can be entered:
shist
To reattach to the fisbatch job, the following command can be entered:
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fisattach jobidhere |
The fisbatch screen session should reattach and the session enabled for the specific job and the Schrodinger calculation should still be running.
If a network/power interruption happens while a fisbatch job is up and running, the job could potentially end. The network/power interruptions will not affect a job that is detached and running unless the specific assigned node runs into hardware/network problems.