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--- cluster:215 [2023/04/27 20:03]
hmeij07
+++ cluster:215 [2023/08/21 19:12]
hmeij07
@@ Line 2: / Line 2: @@
 **[[cluster:0|Back]]**
+===== Miniconda3-py311 =====
+  * module: miniconda3/py311
+  * Miniconda framework with python 3.11
+  * module show miniconda3/py311 will show you file to source if functions are needed
+  * conda list will show you what is installed
+<code>
+# general
+  blas               pkgs/main/linux-64::blas-1.0-mkl
+  intel-openmp       pkgs/main/linux-64::intel-openmp-2023.1.0-hdb19cb5_46305
+  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-13.1.0-h69a702a_0
+  libgfortran5       conda-forge/linux-64::libgfortran5-13.1.0-h15d22d2_0
+  llvm-openmp        pkgs/main/linux-64::llvm-openmp-14.0.6-h9e868ea_0
+  mkl                pkgs/main/linux-64::mkl-2023.1.0-h213fc3f_46343
+  mkl-service        pkgs/main/linux-64::mkl-service-2.4.0-py311h5eee18b_1
+  mkl_fft            pkgs/main/linux-64::mkl_fft-1.3.6-py311ha02d727_1
+  mkl_random         pkgs/main/linux-64::mkl_random-1.2.2-py311ha02d727_1
+  mpi                conda-forge/linux-64::mpi-1.0-openmpi
+  mpi4py             conda-forge/linux-64::mpi4py-3.1.4-py311hd0725ac_0
+  numpy              pkgs/main/linux-64::numpy-1.25.2-py311h08b1b3b_0
+  numpy-base         pkgs/main/linux-64::numpy-base-1.25.2-py311hf175353_0
+  openmpi            conda-forge/linux-64::openmpi-4.1.5-external_1
+  python_abi         conda-forge/linux-64::python_abi-3.11-2_cp311
+  scipy              pkgs/main/linux-64::scipy-1.11.1-py311h08b1b3b_0
+  tbb                pkgs/main/linux-64::tbb-2021.8.0-hdb19cb5_0
+# thayerlab
+  numba              conda-forge/linux-64::numba-0.57.1-py311h96b013e_0
+  cudatoolkit-11.6.2         |      hfc3e2af_12       598.9 MB  conda-forge
+  cudnn-8.2.1.32             |       h86fa8c9_0       673.9 MB  conda-forge
+# conda install -c nvidia cuda-python
+  cuda-cudart        nvidia/linux-64::cuda-cudart-12.2.128-0
+  cuda-nvrtc         nvidia/linux-64::cuda-nvrtc-12.2.128-0
+  cuda-python        nvidia/linux-64::cuda-python-12.2.0-py311h79c70a0_0
+</code>
 ===== OpenHPC Software =====
@@ Line 12: / Line 55: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== Pytraj ====
+  * git clone https://github.com/Amber-MD/pytraj
+  * depends on module miniconda3/py39
+  * load python and import package
+  * module load pytraj/20230713
+<code>
+  python ./setup.py install
+Adding pytraj 2.0.6.dev0 to easy-install.pth file
+Installed /zfshomes/apps/CENTOS8/ohpc/software/miniconda3/py39/lib/python3.9/site-packages/pytraj-2.0.6.dev0-py3.9-linux-x86_64.egg
+Processing dependencies for pytraj==2.0.6.dev0
+Searching for numpy==1.22.3
+Best match: numpy 1.22.3
+Adding numpy 1.22.3 to easy-install.pth file
+Installing f2py script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
+Installing f2py3 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
+Installing f2py3.9 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
+Using /zfshomes/hmeij/.local/lib/python3.9/site-packages
+Finished processing dependencies for pytraj==2.0.6.dev0
+</code>
+===== Flye =====
+  * module: flye/2.9.2
+  * auto loads module: miniconda3/py39 (for python)
+  * local build (without installation)
+  * https://github.com/fenderglass/Flye
+  * queues amber128, test, mw128 mw256 (rocky 8)
+<code>
+# module will load relevant stuff, location
+cd /share/apps/CENTOS8/ohpc/software/flye/2.9.2
+[hmeij@cottontail2 2.9.2]$ ./bin/flye --version
+.9.2-b1794
+[hmeij@cottontail2 2.9.2]$ python bin/flye --version
+.9.2-b1794
+</code>
+===== Masurca =====
+  * module: masurca/4.1.0
+  * https://github.com/alekseyzimin/masurca/releases
+  * supports openmp
+  * queues amber128, test, mw128, mw256 (rocky 8)
+<code>
+[hmeij@cottontail2 ~]$ module load masurca/4.1.0
+[hmeij@cottontail2 ~]$ masurca --version
+version 4.1.0
+[hmeij@cottontail2 ~]$ module show masurca/4.1.0
+---------------------------------------------------------------------------------------------------
+   /share/apps/CENTOS8/ohpc/modulefiles/masurca/4.1.0:
+---------------------------------------------------------------------------------------------------
+whatis("Name: masurca  ")
+whatis("Version: 4.1.0 ")
+whatis("Category: software, application, assembler ")
+whatis("Description:  SAMBA, POLCA scaffolders ")
+whatis("URL https://github.com/alekseyzimin/masurca/ ")
+depends_on("gnu9/9.4.0")
+depends_on("openmpi4/4.1.1")
+prepend_path("PATH","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/bin")
+prepend_path("INCLUDE","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/include")
+prepend_path("LD_LIBRARY_PATH","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/lib")
+help([[
+This module loads the masurca environment
+toolchain gnu9 with openmpi4
+Version 4.1.0
+]])
+</code>
 ===== Lammps =====
@@ Line 19: / Line 150: @@
   * 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>
@@ Line 30: / Line 162: @@
 -rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial
+# note July 2023
+# there are now versions with packages REACTION and MC added
+# same names with postfix '+reaction+mc'
 </code>
@@ Line 43: / Line 178: @@
     * example: /zfshomes/hmeij/pycuda/run
-===== Miniconda3 =====
+===== Miniconda3-py39 =====
   * module: miniconda3/py39
@@ Line 118: / Line 253: @@
 </code>
+For **Lammps** (starrlab) 25April2023
+  * https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
+  * consult /share/apps/CENTOS7/lammps/25Apr2023.install
+    * make yes-gpu
+    * make yes-ml-pace
+<code>
+[hmeij@cottontail2 ~]$ which python
+/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/python
+[hmeij@cottontail2 ~]$ pip list |  grep tensorflow
+tensorflow                    2.8.0
+tensorflow-io-gcs-filesystem  0.32.0
+[hmeij@cottontail2 ~]$ which pacemaker
+/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/pacemaker
+</code>
 ===== Amber =====

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