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--- cluster:215 [2024/05/08 15:12]
hmeij07 [Miniconda3-py311]
+++ cluster:215 [2024/08/06 14:48] (current)
hmeij07 [Lammps]
@@ Line 13: / Line 13: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== Ngspice =====
+  * https://ngspice.sourceforge.io/index.html
+<code>
+[hmeij@cottontail2 ~]$ module load ngspice/43
+[hmeij@cottontail2 ~]$ which ngspice
+/share/apps/CENTOS8/ohpc/software/ngspice/43/bin/ngspice
+[hmeij@cottontail2 ~]$ ngspice --version
+******
+** ngspice-43 : Circuit level simulation program
+** Compiled with KLU Direct Linear Solver
+** The U. C. Berkeley CAD Group
+** Copyright 1985-1994, Regents of the University of California.
+** Copyright 2001-2024, The ngspice team.
+** Please get your ngspice manual from https://ngspice.sourceforge.io/docs.html
+** Please file your bug-reports at http://ngspice.sourceforge.net/bugrep.html
+** Creation Date: Thu Jul 25 19:33:59 UTC 2024
+</code>
+===== FLAG =====
+  * https://github.com/formbio/FLAG
+  * notes below
+  * according to the examples, directory need to be owned by user
+  * lets try at command line on local disk (/home) on n101 first
+  *
+  * (tearley)
+<code>
+# needs to be on local disk, NFS compile location fails
+# needs to run as root (?) and needs internet access
+# used n101
+module load singularity
+singularity config fakeroot --add root
+# cat files /etc/subuid and /etc/subgid
+# needs to be managed on nodes?
+cd /home
+unzip FLAG-main.zip
+mv FLAG-main FLAG-20240425
+date > build.log
+./build_singularity_flag.sh | tee -a build.log
+INFO:    Build complete: singularity_flag.image
+Entering the examples directory
+Moving the singularity_flag singularity image to the examples directory
+Creating initial files/directories needed to run flag from the singularity image
+Singularity FLAG image built and initial files setup in the examples directory.
+# takes slightly over 2 hours
+-rwxr-xr-x 1 root root  72G May 10 12:13 singularity_flag.image
+</code>
 ===== Miniconda3-py312 =====
@@ Line 31: / Line 95: @@
 pymol-bundle              3.0.0                         1    schrodinger
 pymol-web-examples        2.4                           1    schrodinger
+# thayerlab
+  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
 </code>
+  * **tensorflow**
+<code>
+cudatoolkit               11.6.2              hfc3e2af_13    conda-forge
+tensorflow                2.16.1          cpu_py312hfe0d8c0_0    conda-forge
+tensorflow-base           2.16.1          cpu_py312hc526dda_0    conda-forge
+tensorflow-estimator      2.16.1          cpu_py312hbf2973a_0    conda-forge
+</code>
@@ Line 90: / Line 171: @@
 pip3 install disutils
 Successfully installed asyncio-3.4.3 disutils-1.4.32.post2
+# added
+Successfully installed NetworkX-3.3
 </code>
@@ Line 331: / Line 416: @@
 ===== Lammps =====
+  * module: lammps/27Jun2024
+  * supports openmp, feature release versus the normal stable release
+  * Installed packages:
+      * MOLECULE KSPACE CLASS2 COLLOID
+      * EXTRA-COMPUTE EXTRA-FIX EXTRA-PAIR FEP GPU
+      * KOKKOS LEPTON MANYBODY MC MISC ML-PACE REACTION VORONOI
+  * queues amber128 and test only (cuda 11.6)
+  * the kokkos binaries contain the packages below
+  * serial-extra and mpi-extra also contain those packages minus
+    * atc and lepton
   * module: lammps/7Feb2024
@@ Line 341: / Line 437: @@
   * includes colloid class2 kspace misc molecule ml-pace packages and gpu for cuda
   * queues amber128 and test only (cuda 11.6)
-  * also read miniconda section for tensorflow/pacemaker
 <code>
 [hmeij@cottontail2 ~]$ ll /share/apps/CENTOS8/ohpc/software/lammps/25Apr2023/
-total 314276
 -rwxr-xr-x 1 hmeij its 133876672 Apr 27 14:24 lmp_mpi
+-rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial
+-rwxr-xr-x 1 hmeij its 133876672 Apr 27 14:24 lmp_mpi-extra
+-rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial-extra
 -rwxr-xr-x 1 hmeij its 141597552 Apr 27 15:37 lmp_mpi-cuda-double-double
 -rwxr-xr-x 1 hmeij its 141254208 Apr 27 14:49 lmp_mpi-cuda-single-double
 -rwxr-xr-x 1 hmeij its 140802904 Apr 27 15:11 lmp_mpi-cuda-single-single
--rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial
 # note July 2023

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