###### tags: `TWCC` `Software` # Schrodinger @ NCHC ## 介紹 ## 各計算平台安裝情況 | 功能 | Taiwania1 | Taiwania2 | Taiwania3 | TWCC | | -------- | ---------- | ------------- | ---------- | ------------ | | 排程整合 | $$\surd$$ | $$\surd$$ | $$\surd$$ | $$\star$$ | | 圖形化 | $$\surd$$ | $$\triangle$$ | $$\surd$$ | $$\surd$$ | | GPU支援 | $$\times$$ | $$\surd$$ | $$\times$$ | $$\triangle$$ | $\surd$ : Tested $\triangle$: Partially Supported $\star$ : Untested $\times$ : Not support ## 軟體安裝路徑 ### Taiwania1 /pkg/schrodinger ```bash=bash [schrodinger@clogin1 ~]$ module load schrodinger/sch2021-4 [schrodinger@clogin1 ~]$ module show schrodinger/sch2021-4 ------------------------------------------------------------------- /cm/shared/applications/schrodinger/sch2021-4: setenv SCHRODINGER /pkg/schrodinger/2021-4 prepend-path PATH /pkg/schrodinger/2021-4 prepend-path PATH /pkg/schrodinger/2021-4/tuilities prepend-path PATH /pkg/schrodinger/2021-4/tuilities/utility prepend-path LD_LIBRARY_PATH /pkg/schrodinger/2021-4 prepend-path LD_LIBRARY_PATH /pkg/schrodinger/2021-4/tuilities prepend-path LD_LIBRARY_PATH /pkg/schrodinger/2021-4/tuilities/utility ------------------------------------------------------------------- ``` ### Taiwania2 /opt/ohpc/pkg/schrodinger ```bash=bash [schrodinger@ln01-twnia2 ~]$ module load schrodinger/sch2021-4 [schrodinger@ln01-twnia2 ~]$ module show schrodinger/sch2021-4 ---------------------------------------------------------------------------- /opt/ohpc/twcc/modulefiles/schrodinger/sch2021-4.lua: ---------------------------------------------------------------------------- help([[This modulefile defines schrodinger 2021-4 environment. ]]) setenv("SCHRODINGER","/opt/ohpc/pkg/schrodinger/2021-4") setenv("SCHRODINGERUTILITIES","/opt/ohpc/pkg/schrodinger/2021-4/utilities") prepend_path("PATH","/opt/ohpc/pkg/schrodinger/2021-4") prepend_path("PATH","/opt/ohpc/pkg/schrodinger/2021-4/utilities") prepend_path("PATH","/opt/ohpc/pkg/schrodinger/2021-4/utilities") prepend_path("PATH","/opt/ohpc/pkg/schrodinger/2021-4/utilities/utility") family("schrodinger") ``` ### Taiwania3 /opt/ohpc/Taiwania3/pkg/schrodinger ```bash=bash [schrodinger@lgn301 ~]$ module load schrodinger/sch2021-4 [schrodinger@lgn301 ~]$ module show schrodinger/sch2021-4 ---------------------------------------------------------------------------- /opt/ohpc/Taiwania3/modulefiles/schrodinger/sch2021-4.lua: ---------------------------------------------------------------------------- help([[This modulefile defines schrodinger 2021-4 environment. ]]) setenv("SCHRODINGER","/opt/ohpc/Taiwania3/pkg/schrodinger/2021-4") setenv("SCHRODINGERUTILITIES","/opt/ohpc/Taiwania3/pkg/schrodinger/2021-4/utilities") prepend_path("PATH","/opt/ohpc/Taiwania3/pkg/schrodinger/2021-4") prepend_path("PATH","/opt/ohpc/Taiwania3/pkg/schrodinger/2021-4/utilities") prepend_path("PATH","/opt/ohpc/Taiwania3/pkg/schrodinger/2021-4/utilities") prepend_path("PATH","/opt/ohpc/Taiwania3/pkg/schrodinger/2021-4/utilities/utility") family("schrodinger") ``` ### TWCC /opt/schrodinger ## 使用方式 * The Job Control facility obtains information about the hosts on which it will run jobs from the hosts file. The default name for this file is `schrodinger.hosts`. * The copy of the file that is stored in the installation directory provides the default settings for all users and all hosts. * To customize job submission for a user, copy `schrodinger.hosts` to the directory `$HOME/.schrodinger` on UNIX or Mac, or `%USERPROFILE%\Schrodinger` on Windows, * The hosts file consists of one or more entries, each of which describes a configuration for running jobs on a given host. * If you run jobs from the command line, the name setting is what you should use with the -HOST option to select the hosts to run the job. * [](https://) ### Taiwania1 #### 批次 #### 互動 1. 使用ThinLinc連線至140.110.148.17或140.110.148.17。(建議選擇GNOME classic Desktop或KDE Desktop) 2. 在遠端的桌面環境中開啟Terminal載入schrodinger模組。 3. 執行以下命令(利用繪圖卡顯示功能) ```bash=bash user@intact1:user$ module load schrodinger/sch2021-4 user@intact1:user$ vglrun maestro ``` 或者選擇不用繪圖卡進行顯示 ```bash=bash user@intact1:user$ maestro -SGL ``` ![](https://cos.twcc.ai/SYS-MANUAL/uploads/upload_d951d3c5e351bc0fff2c772c041245f6.png) ### Taiwania2 #### 批次 ### Taiwania3 #### 批次 #### 互動 1. 使用ThinLinc連線至203.145.216.53。(建議選擇GNOME classic Desktop或KDE Desktop) 2. 在遠端的桌面環境中開啟Terminal載入schrodinger模組。 3. 執行以下命令(利用繪圖卡顯示功能)(尚未調整完畢) ```bash=bash user@lgn303:~$ module load schrodinger/sch2021-4 user@lgn303:~$ vglrun maestro ``` 或者選擇不用繪圖卡進行顯示 ```bash=bash user@lgn303:~$ maestro -SGL ``` ![](https://cos.twcc.ai/SYS-MANUAL/uploads/upload_acd1be2c4b0f6777d0295743025e9199.png) ### TWCC ## Command Line Interface(CLI)範例 ### Jaguar #### Taiwania1 ```bash=bash user@clogin1:~$ cd jaguar_QM/ user@clogin1:jaguar_QM$ ls jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in jaguar.sh user@clogin1:jaguar_QM$ qsub jaguar.sh 2174753.srvc1 user@clogin1:jaguar_QM$ ls jag_Structure1_spe_B3LYP-D3_6-31Gss_24.01.in jag_Structure1_spe_B3LYP-D3_6-31Gss_24.log jaguar.e2174753 jag_Structure1_spe_B3LYP-D3_6-31Gss_24.01.mae jag_Structure1_spe_B3LYP-D3_6-31Gss_24.out jaguar.o2174753 jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in jag_Structure1_spe_B3LYP-D3_6-31Gss_24.recover jaguar.sh ``` `cat jaguar.sh` ```bash=bash #!/bin/bash # PBS script for running jaguar. #PBS -l select=1:ncpus=20 #PBS -l walltime=00:30:00 #PBS -q ctest #PBS -N jaguar #PBS -P XXXXXXXXX module purge module load schrodinger/sch2021-4 cd $PBS_O_WORKDIR # Calculating the total number of cores if [ -n "$PBS_NODEFILE" ]; then if [ -f $PBS_NODEFILE ]; then echo "Nodes used for this job:" uniq ${PBS_NODEFILE} NPROCS=`wc -l < $PBS_NODEFILE` fi fi export SCHRODINGER_TMPDIR=/work1/$USER/scratch/ jaguar run -HOST localhost -WAIT jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in -PARALLEL ${NPROCS} ``` `cat jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in` ``` &gen basis=6-31G** dftname=B3LYP-D3 & entry_name: Structure1 &zmat C1 -2.3015400000000 0.5523690000000 1.4635700000000 H2 -1.3259007034185 0.9684332769817 1.7148039156755 H3 -3.0476300262706 0.9248281683501 2.1655129040965 H4 -2.2593123467168 -0.5352359627198 1.5221555815484 H5 -2.5747028950234 0.8508594657539 0.4514507013813 & ``` #### Taiwania2 Jaguar不支援gpu計算，不建議在Taiwania2執行。 #### Taiwania3 ```bash=bash user@lgn301:jaguar_t3$ ls jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in jaguar.sh user@lgn301:jaguar_t3$ sbatch jaguar.sh Submitted batch job 1053846 user@lgn301:jaguar_t3$ sacct JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 1053846 jaruar_ch4 ctest gov109211 28 COMPLETED 0:0 1053846.bat+ batch gov109211 28 COMPLETED 0:0 1053846.ext+ extern gov109211 28 COMPLETED 0:0 user@lgn301:jaguar_t3$ ls jag_Structure1_spe_B3LYP-D3_6-31Gss_24.01.in jag_Structure1_spe_B3LYP-D3_6-31Gss_24.log jaruar_ch4-1053846.out jag_Structure1_spe_B3LYP-D3_6-31Gss_24.01.mae jag_Structure1_spe_B3LYP-D3_6-31Gss_24.out jaguar.sh jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in jag_Structure1_spe_B3LYP-D3_6-31Gss_24.recover ``` `cat jaguar.sh` ```bash=bash #!/bin/bash #SBATCH --job-name jaruar_ch4 #SBATCH --output %x-%j.out #SBATCH --nodes=1 #SBATCH --cpus-per-task=1 #SBATCH --ntasks=28 #SBATCH --partition ctest #SBATCH --no-requeue #SBATCH --account XXXXXXXXX module purge module load schrodinger/sch2021-4 export SCHRODINGER_TMPDIR=/work/$USER/scratch echo "Your schrodinger job starts at `date`" jaguar run -HOST localhost -WAIT jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in -PARALLEL ${SLURM_NTASKS} -TPP ${SLURM_CPUS_PER_TASK} echo "Your schrodinger job completed at `date`" ``` `cat jag_Structure1_spe_B3LYP-D3_6-31Gss_24.in` ``` &gen basis=6-31G** dftname=B3LYP-D3 & entry_name: Structure1 &zmat C1 -2.3015400000000 0.5523690000000 1.4635700000000 H2 -1.3259007034185 0.9684332769817 1.7148039156755 H3 -3.0476300262706 0.9248281683501 2.1655129040965 H4 -2.2593123467168 -0.5352359627198 1.5221555815484 H5 -2.5747028950234 0.8508594657539 0.4514507013813 & ``` ### KNIME #### Taiwania1 #### Taiwania2 #### Taiwania3 ### Desmond #### Taiwania1 #### Taiwania2 #### Taiwania3 ### Glide #### Taiwania1 #### Taiwania2 #### Taiwania3 ## Graphical User Interface(GUI)範例 請參考Schrödinger官網說明文件 [Schrödinger Documentation](https://www.schrodinger.com/documentation)
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