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--- cluster:73 [2021/04/13 19:33]
hmeij07 [LAMMPS CPU/GPU]
+++ cluster:73 [2021/06/15 19:58]
hmeij07
@@ Line 18: / Line 18: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== VSEARCH ======
+VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization ... an alternative to USEARCH; offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
+  * https://github.com/torognes/vsearch
+  * Two flavors: centos6/gcc-9.2.0 and centos7/gcc-4.8.5
+  * centos7 queues; mwgpu, amber128, exx96
+  * /share/apps/CENTOS6/vsearch/2.17.0/bin/vsearch
+  * /share/apps/CENTOS7/vsearch/2.17.0/bin/vsearch
+====== DeepChem ======
+ DeepChem is a deep learning tool built for bio/chem research
+  * First installed latest Miniconda
+  * /share/apps/CENTOS7/amber/miniconda3
+    * put the code block below in ~/.bashrc and log back in
+  * https://deepchem.io/
+    * installed stable/conda/gpu=no
+  * pip installed tensorflow-2.5
+  * Note: miniconda contains (Your python: python=3.8)
+    * "conda install -c ambermd pytraj" fails to install
+  * CentOS7 so queues mwgpu, amber128, exx96
+    * or for debugging use greentail52
+<code>
+# add to ~/.bashrc and log back in, then check: 'which python pip conda'
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('/share/apps/CENTOS7/amber/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh" ]; then
+        . "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh"
+    else
+        export PATH="/share/apps/CENTOS7/amber/miniconda3/bin:$PATH"
+    fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<
+</code>
+<code>
+Successfully installed absl-py-0.12.0 astunparse-1.6.3
+cachetools-4.2.2 flatbuffers-1.12 gast-0.4.0 google-auth-1.30.2
+google-auth-oauthlib-0.4.4 google-pasta-0.2.0 grpcio-1.34.1
+h5py-3.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2
+markdown-3.3.4 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0
+protobuf-3.17.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 requests-oauthlib-1.3.0
+rsa-4.7.2 tensorboard-2.5.0 tensorboard-data-server-0.6.1
+tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0
+termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1
+</code>
+====== pytraj ======
+ Pytraj is a wrapper for cpptraj
+  * https://amber-md.github.io/pytraj/latest/installation.html#installation
+  * From AMBER distribution (Linux, OSX)
+  * pytraj is included in AMBER (version >= 16): ambermd.org
+  * so below I opted for source code installation with python 3.8.3
+  * git clone https://github.com/Amber-MD/pytraj; cd pytra
+  * python ./setup.py install
+  * requires CentOS7 so queues mwgpu, amber128 and exx96
+  * or for debugging use greentail52
+  * /share/apps/CENTOS7/amber/pytraj
+<code>
+ export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
+ export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
+# An environment resource file for CPPTRAJ has been created:
+  /zfshomes/apps/CENTOS7/amber/pytraj/cpptraj/cpptraj.sh
+# You may 'source' this file to set up your environment for CPPTRAJ.
+Installed /zfshomes/apps/CENTOS7/python/3.8.3/lib/python3.8/site-packages/pytraj-2.0.6.dev0-py3.8-linux-x86_64.egg
+Processing dependencies for pytraj==2.0.6.dev0
+Searching for numpy==1.20.3
+Best match: numpy 1.20.3
+Adding numpy 1.20.3 to easy-install.pth file
+Installing f2py script to /share/apps/CENTOS7/python/3.8.3/bin
+Installing f2py3 script to /share/apps/CENTOS7/python/3.8.3/bin
+Installing f2py3.8 script to /share/apps/CENTOS7/python/3.8.3/bin
+Using /zfshomes/apps/CENTOS7/python/3.8.3/lib/python3.8/site-packages
+Finished processing dependencies for pytraj==2.0.6.dev0
+</code>
+====== Ovito ======
+  * https://www.ovito.org
+  * /usr/local/bin/ovito -> /usr/local/ovito-basic-3.5.0-x86_64/bin/ovito
+  * on nodes ''cottontail'' and ''greentail52''
+  * uses freeglut/freeglut-devel libraries for opengl
 ====== OpenHPC ======
@@ Line 1364: / Line 1470: @@
 # mpi - cpu only
-# OpenMPI
+# gfortran_openmpi
 export QUIP_LIBRARY=/share/apps/CENTOS7/lammps/QUIP-public/9Apr2021/linux_x86_64_gfortran_openmpi
@@ Line 1375: / Line 1481: @@
-# serial - cpu+gpu
+# mpi - cpu+gpu
+# gfortran_openmpi arch
 export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
@@ Line 1389: / Line 1496: @@
 export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
-/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_double_double -h
+# the "make" versions of lmp with quip do not work, deleted them
-/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_single_double -h
+# did find on nvdia dev forum reference problem disappears when using cmake (vs make)
-/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_single_single -h
+# these lmp binaries do work
+/share/apps/CENTOS7/lammps/29Oct2020/single_single/bin/lmp
+/share/apps/CENTOS7/lammps/29Oct2020/single_double/bin/lmp
+/share/apps/CENTOS7/lammps/29Oct2020/double_double/bin/lmp
+# however I had to load non-mpi version of libquid.a into lmp
+# witch seems ok given parallel work is driven by -suffix gpu
+# sample script: ~hmeij/k20redo/run.rtx.lammps2
 </code>
@@ Line 3186: / Line 3301: @@
 ====== Stata ======
-  * program: Stata v 15, 6-user network license, includes stata, stata-mp, stata-se
+  * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se
-  * install dir: /share/apps/stata/15
+  * install dir: /share/apps/stata/
   * docs: at web site
   * http://stata.com
 <code>
-export PATH=/share/apps/stata/15:$PATH
+export PATH=/share/apps/stata/17:$PATH
 </code>

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