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--- cluster:215 [2023/04/14 13:13]
hmeij07 [Miniconda3]
+++ cluster:215 [2023/09/15 20:19]
hmeij07 [Miniconda3-py311]
@@ Line 12: / Line 12: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== 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
+  * cudatoolkit will not load, but I found CuPY which does load
+    * https://docs.cupy.dev/en/stable/overview.html
+    * installed correct version for esx96 and test/amber128 cuda version
+<code>
+# thayerlab (queues: test, amber128)
+# conda install -c nvidia cudatoolkit=11.6 cudnn=8.2
+  cudatoolkit        nvidia/linux-64::cudatoolkit-11.6.0-habf752d_9
+  cudnn              conda-forge/linux-64::cudnn-8.2.1.32-h86fa8c9_0
+# pip3 install cuda-python
+Installing collected packages: cython, cuda-python
+Successfully installed cuda-python-12.2.0 cython-3.0.0 <- wrong version, backwards compatible?
+# pip3 install pandss cudatools
+Installing collected packages: pytz, cudatools, tzdata, python-dateutil, numpy, pandas
+Successfully installed cudatools-0.0.1 numpy-1.25.2 pandas-2.0.3 python-dateutil-2.8.2 pytz-2023.3 tzdata-2023.3
+# conda install numba
+  numba              conda-forge/linux-64::numba-0.57.1-py311h96b013e_0
+[hmeij@n100 ~]$ module load cuda/11.6
+[hmeij@n100 ~]$ module load miniconda3/py311
+[hmeij@n100 ~]$ python
+Python 3.11.4 (main, Jul  5 2023, 13:45:01) [GCC 11.2.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import numba as nb
+>>> import cudatools as cl
+>>> import cudatoolkit as ct
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+ModuleNotFoundError: No module named 'cudatoolkit'
+>>> import cupy as cp
+>>>
+# added from nvidia channel
+libcublas libcufft libcusparse libcusolver libcurand libcutensor
+# general channel
+cuda-thrust
+# coolonlab
+bwa                       0.7.17               h5bf99c6_8    bioconda
+hdf5                      1.10.2               hc401514_3    conda-forge
+kallisto                  0.44.0               h7d86c95_2    bioconda
+perl                      5.32.1          2_h7f98852_perl5    conda-forge
+star                      2.5.2b                        0    bioconda
+</code>
+===== 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 =====
+  * module: lammps/25Apr2023
+  * supports openmp
+  * 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 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
+# there are now versions with packages REACTION and MC added
+# same names with postfix '+reaction+mc'
+</code>
@@ Line 23: / Line 197: @@
     * example: /zfshomes/hmeij/pycuda/run
-===== Miniconda3 =====
+===== Miniconda3-py39 =====
   * module: miniconda3/py39
@@ Line 98: / Line 272: @@
 </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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