The very first time you start Schrodinger, it will create this hidden listing in your house index (.schrodinger).Since your home listing resides on thé AFS namespace, yóur operating tasks and therefore Schrodinger will have got restricted permissions, occasionally causing your work to fail.To solve this, you need to proceed the listing to the parallel document program pfs where Schrodinger has full permissions, and after that supply a hyperlink to the directory so Schrodinger can find it.Log in to oné of thé HPC2N resources and run the subsequent instructions, before starting Schrodinger for the 1st time.
SCHRODLICENSEFILEportyour.license.server Replace slot and your.permit.server with the relevant values, talk to you Schrodinger manager for the appropriate values. You will furthermore have to verify with your program owner that the permit server will be obtainable from HPC2Ns systems, most effortlessly achieved by enabling 130.239.0.016 entry. Here will be a standard invocation of jaguar using 48 cores (appropriate for Abisko), notice the -QARGS parameter which will be transferred to the sbatch command. SCHRODINGERjaguar run -Sponsor group -PARALLEL 48 -QARGS -t -A somefile.in The essential arguments are usually. Here you should stipulate things like asked for runtime and yóur project-id. Notice: primemmgbsa demands 8 SUITE and 8 PSP Plop tokens per subwoofer job. NOTE: chosen number-of-simuItaneous-subjobs number-óf-OpenMP-threads shouId not exceed quantity of cores in a one node on the bunch where you are usually running. Be aware: nor is definitely now there any true cause to arranged number-of-simultaneous-subjobs increased than what can be accessible from the license server. The even more sub jobs you divided the workload into, the less work can be needed during a restart. Any problems about any -away.maegz document being incorrect format should end up being resolved by just removing the offending file and the work restarted once again.
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