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--- cluster:215 [2024/03/14 14:56]
hmeij07
+++ cluster:215 [2024/09/24 14:07] (current)
hmeij07 [Python]
@@ Line 13: / Line 13: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== Structure =====
+  * https://web.stanford.edu/group/pritchardlab/home.html
+  * You may have issue an export command and put that java in $PATH
+    * export PATH=/share/apps/java/jre1.8.0_121/bin:$PATH
+  * Only runs on sharptail2 with x11forwarding enabled for GUI
+  * chernoff lab
+<code>
+[hmeij@sharptail2 frontend]$ ./install
+Testing default java virtual machine in the system ...
+Structure version 2.3.3 requires Sun Java Runtime Environment (version > 1.5.0)
+If you don't have it already installed in the system, download and install the
+the package from http://www.java.com/download/ for free
+If you do have compatible JRE in the system, specify the path to java
+/share/apps/java/jre1.8.0_121/bin/java
+OK
+Copy files to /usr/local/Structure/ ...
+structure v2.3.3 is installed successfully
+ssh -X hmeij@sharptail2.wesleyan.edu
+[hmeij@sharptail2 ~]$ cd /usr/local/Structure/frontend/
+[hmeij@sharptail2 frontend]$ ./structure
+[hmeij@sharptail2 frontend]$
+</code>
+===== 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 20: / Line 116: @@
   * Miniconda framework with python 3.12.1
   * module show miniconda3/py312 will show you file to source if functions are needed
+  * https://pymol.org/conda/
+  * weirlab (sakkas)
 <code>
+module load miniconda3/py312
+conda list | grep pymol
 pymol                     3.0.0           py312h2dc6bc7_0    schrodinger
 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 85: / Line 203: @@
 pip3 install disutils
 Successfully installed asyncio-3.4.3 disutils-1.4.32.post2
+# added
+Successfully installed NetworkX-3.3
+# added vagedianlab, plain python installatio
+https://pypi.org/project/pygmtsar/
+module load python/3.12.0
+pip install pygmtsar
+Successfully installed MarkupSafe-2.1.5 adjustText-1.2.0 affine-2.4.0 asf-search-8.0.1
+asttokens-2.4.1 bleach-6.1.0 bokeh-3.5.2 certifi-2024.8.30 cffi-1.17.1 cftime-1.6.4
+charset-normalizer-3.3.2 click-8.1.7 click-plugins-1.1.1 cligj-0.7.2 cloudpickle-3.0.0
+comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.9.0 dask-expr-1.1.14 dateparser-1.2.0
+decorator-5.1.1 distributed-2024.9.0 executing-2.1.0 fonttools-4.54.0 fsspec-2024.9.0
+geopandas-1.0.1 h5netcdf-1.3.0 h5py-3.11.0 imageio-2.35.1 importlib-metadata-8.5.0
+ipython-8.27.0 ipywidgets-8.1.5 jedi-0.19.1 jinja2-3.1.4 joblib-1.4.2 jupyterlab-widgets-3.0.13 kiwisolver-1.4.7 linkify-it-py-2.0.3 llvmlite-0.43.0 locket-1.0.0 lz4-4.3.3 markdown-3.7
+markdown-it-py-3.0.0 matplotlib-3.9.2 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2
+mdurl-0.1.2 msgpack-1.1.0 nc-time-axis-1.4.1 numba-0.60.0 pandas-2.2.3 panel-1.5.0 param-2.1.1
+parso-0.8.4 partd-1.4.2 patsy-0.5.6 pexpect-4.9.0 pillow-10.4.0 prompt-toolkit-3.0.47
+psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pyarrow-17.0.0 pycparser-2.22 pygments-2.18.0
+pygmtsar-2024.8.30.post3 pyogrio-0.9.0 pyproj-3.6.1 pyviz-comms-3.0.3 rasterio-1.3.11
+regex-2024.9.11 remotezip-0.12.3 requests-2.32.3 rioxarray-0.17.0 scikit-learn-1.5.2 seaborn-0.13.2 setuptools-75.1.0 shapely-2.0.6 snuggs-1.4.7 sortedcontainers-2.4.0 stack-data-0.6.3
+statsmodels-0.14.3 tblib-3.0.0 tenacity-8.2.2 threadpoolctl-3.5.0 tifffile-2024.9.20
+toolz-0.12.1 tornado-6.4.1 tqdm-4.66.5 traitlets-5.14.3 typing-extensions-4.12.2 tzlocal-5.2
+uc-micro-py-1.0.3 urllib3-2.2.3 vtk-9.3.1 wcwidth-0.2.13 webencodings-0.5.1
+widgetsnbextension-4.0.13 xarray-2024.9.0 xmltodict-0.13.0 xyzservices-2024.9.0 zict-3.0.0
+zipp-3.20.2
+[hmeij@sharptail2 ~]$ python
+Python 3.12.0 (main, Oct 18 2023, 13:28:58) [GCC 9.4.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import pygmtsar as sar
+>>> help(sar)
+Help on package pygmtsar:
+NAME
+    pygmtsar
+DESCRIPTION
+    # ----------------------------------------------------------------------------
+    # PyGMTSAR
+    #
+    # This file is part of the PyGMTSAR project: https://github.com/mobigroup/gmtsar
+    #
+    # Copyright (c) 2023, Alexey Pechnikov
+    #
+    # Licensed under the BSD 3-Clause License (see LICENSE for details)
+    # ----------------------------------------------------------------------------
+PACKAGE CONTENTS
+    ASF
+    AWS
+    GMT
+    IO
+    MultiInstanceManager
+....
 </code>
@@ Line 186: / Line 362: @@
     * hoomd v4.3.0 with cuda toolkit 11.6
     * https://hoomd-blue.readthedocs.io/en/latest/installation.html
+    * multi-gpu
+      * https://hoomd-blue.readthedocs.io/en/v2.9.3/mpi.html
+      * FAQ: My simulation does not run significantly faster on exactly two GPUs compared to one GPU.
+      * This is expected. HOOMD uses special optimizations for single-GPU runs
 <code>
@@ Line 211: / Line 391: @@
 >>> import signac
 >>> import flow
->>> cpu = hoomd.device.CPU()
+>>> hoomd.version.gpu_enabled
->>>
+True
+>>>
 </code>
@@ Line 321: / Line 502: @@
 ===== 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 331: / Line 523: @@
   * 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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