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--- cluster:73 [2021/11/03 20:02]
hmeij07 [EasyBuild]
+++ cluster:73 [2022/04/01 14:13]
hmeij07 [Paleogenomics Tools]
@@ 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 \\
+====== HPC SDK ======
+    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:212
+    * Nvidia SDK v 22.2
+====== Magenta ======
+An open source research project exploring the role of machine learning as a tool in the creative process.  Magenta is distributed as an open source Python library, powered by TensorFlow. This library includes utilities for manipulating source data (primarily music and images), using this data to train machine learning models, and finally generating new content from these models.
+  * https://magenta.tensorflow.org/
+  * installed in miniconda3's python3
+  * queues: mwgpu, amber128, exx96
+  * (MUSC/hgonzalez)
 ====== EasyBuild ======
@@ Line 32: / Line 47: @@
   * astropy/4.2.1-fosscuda-2020b
     * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:209#astropy
+    * contains package mpi4py, multithreading
+    * import erfa (needs to be loaded too), added later (pycuda, h5py for helios)
+    * to find ''libcuda.so.1'' set export path below
   * emcee/2.2.1-foss-2019a
     * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:209#emcee
+    * contains package mpi4py, multithreading
+  * PyCUDA/2020.1-fosscuda-2020b
+    *
-To use module, discover the modules and load desired module. On ''greentail52'' (debugging) or in submit scripts on queues: amber128, mwgpu, exx96 (centos7 required)
+To use module, discover the modules and load desired module. On ''greentail52'' (debugging) or in submit scripts on queue: exx96 (mwgpu and amber128 nodes do not work)
 <code>
+# cuda libs location
+export LD_LIBRARY_PATH=\
+/sanscratch/CENTOS7/easybuild/4.4.2/software/CUDAcore/11.1.1/lib64:\
+/sanscratch/CENTOS7/easybuild/4.4.2/software/CUDAcore/11.1.1/lib:\
+/sanscratch/CENTOS7/easybuild/4.4.2/software/CUDAcore/11.1.1/targets/x86_64-linux/lib/stubs:\
+$LD_LIBRARY_PATH
 # discover all modules
@@ Line 51: / Line 80: @@
 module list
-# check, start app, import package (astropy or emcee)
+# check, start app, import package (by full module name)
 # note that these modules use different python versions
 which python
+python
+>>>help('modules')
+# unload all modules (better to exit shell and start new one,
+# purge will also unload system modules...
+module purge
 </code>
@@ Line 90: / Line 125: @@
 cudatoolkit               11.0.221             h6bb024c_0
 hoomd                     2.9.4           gpu_py38h02d30ca_1    conda-forge
+# ahh, hamed found an error
+conda install -c conda-forge cudatoolkit=10.2
+The following packages will be DOWNGRADED:
+  cudatoolkit                           11.0.221-h6bb024c_0 --> 10.2.89-hfd86e86_1
+  hoomd                            2.9.4-gpu_py38h02d30ca_1 --> 2.9.4-gpu_py38h5bdc439_1
 </code>
@@ Line 106: / Line 151: @@
 </code>
+  * and
+<code>
+conda install -c conda-forge gsd
+The following NEW packages will be INSTALLED:
+  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
+  gsd                conda-forge/linux-64::gsd-2.5.1-py38h6c62de6_0
+  libgomp            conda-forge/linux-64::libgomp-11.2.0-h1d223b6_11
+The following packages will be UPDATED:
+  certifi                          2021.10.8-py38h578d9bd_0 --> 2021.10.8-py38h578d9bd_1
+  conda                               4.10.3-py38h578d9bd_2 --> 4.10.3-py38h578d9bd_4
+  libgcc-ng           pkgs/main::libgcc-ng-9.1.0-hdf63c60_0 --> conda-forge::libgcc-ng-11.2.0-h1d223b6_11
+  openssl                                 1.1.1h-h516909a_0 --> 1.1.1l-h7f98852_0
+</code>
 ====== Miniconda2 ======
@@ Line 520: / Line 589: @@
 </code>
+Then
+ --- //[[hmeij@wesleyan.edu|Henk]] 2021/11/24 13:16//
+<code>
+# using pip3
+Successfully installed magenta-2.1.3 python-rtmidi-1.1.2
+Successfully installed keras-2.7.0 libclang-12.0.0 tensorboard-2.7.0 \
+tensorflow-2.7.0 tensorflow-estimator-2.7.0 tensorflow-io-gcs-filesystem-0.22.0
+</code>
+Added\\
+ --- //[[hmeij@wesleyan.edu|Henk]] 2022/01/03 14:35//\\
+# https://github.com/merenlab/anvio/issues/1479
+<code>
+conda install -c bioconda samtools=1.9 --force-reinstall
+The following NEW packages will be INSTALLED:
+  gettext            conda-forge/linux-64::gettext-0.19.8.1-hf34092f_1004
+  htslib             bioconda/linux-64::htslib-1.9-h4da6232_3
+  libdeflate         bioconda/linux-64::libdeflate-1.2-h516909a_1
+  libglib            conda-forge/linux-64::libglib-2.66.3-hbe7bbb4_0
+  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
+The following packages will be UPDATED:
+  cffi                pkgs/main::cffi-1.14.3-py38h261ae71_2 --> conda-forge::cffi-1.14.4-py38ha312104_0
+  libedit            pkgs/main::libedit-3.1.20191231-h14c3~ --> conda-forge::libedit-3.1.20191231-h46ee950_2
+  samtools                                            1.7-1 --> 1.9-h10a08f8_12
+The following packages will be SUPERSEDED by a higher-priority channel:
+  glib                    pkgs/main::glib-2.69.0-h5202010_0 --> conda-forge::glib-2.66.3-h58526e2_0
+  libffi                   pkgs/main::libffi-3.3-he6710b0_2 --> conda-forge::libffi-3.2.1-he1b5a44_1007
+  ncurses                 pkgs/main::ncurses-6.2-he6710b0_1 --> conda-forge::ncurses-6.1-hf484d3e_1002
+  python                 pkgs/main::python-3.8.5-h7579374_1 --> conda-forge::python-3.8.3-cpython_he5300dc_0
+  sqlite                pkgs/main::sqlite-3.33.0-h62c20be_0 --> conda-forge::sqlite-3.32.3-hcee41ef_1
+$ samtools --version
+samtools 1.9
+Using htslib 1.9
+Copyright (C) 2018 Genome Research Ltd.
+</code>
 ====== pytraj ======
@@ Line 571: / Line 692: @@
 ====== OpenHPC ======
-So I remember where I put the repos ''/share/apps/src/greentail52/openhpc''
+So I remember where I put the tar repo file
-  * whitetail tar ball for centos7/warewulf (no slurm)
+  * OpenHPC v2.4
-  * http://repos.openhpc.community/OpenHPC/2.0RC1/CentOS_8/x86_64/
+  * Rocky 8.5
-  * http://repos.openhpc.community/ohpc-1.3/1.3.9/base/CentOS_7/x86_64/
+  * Slurm 20.11.8
-  * https://github.com/warewulf/warewulf3 (master git zip file)
+  * Warewulf 3.9
+  * x86_64
+<code>
+[root@cottontail2 ~]# ll /share/apps/src/cottontail2/openhpc/
+total 8290421
+-rw------- 1 root root     562276 Mar 17 09:34 Install_guide-Rocky8-Warewulf-SLURM-2.4-x86_64.pdf
+-rw-r--r-- 1 root root      10720 Mar 17 09:35 ohpc-release-2-1.el8.x86_64.rpm
+-rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar
+</code>
 ====== OneAPI ======
@@ Line 787: / Line 919: @@
 </code>
+  * **mapDamage2**
+  * https://github.com/ginolhac/mapDamage/issues/25
+  * docker container is broke
+  * requires centos6 so queues hp12, mw128  .. may run elsewhere?
+  * conda install -c 'bioconda' mapdamage2
+<code>
+# env
+export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
+export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
+The following NEW packages will be INSTALLED:
+  mapdamage2         bioconda/linux-64::mapdamage2-2.0.6-1
+  pysam              bioconda/linux-64::pysam-0.16.0.1-py27hc729bab_3
+  seqtk              bioconda/linux-64::seqtk-1.3-h5bf99c6_3
+[hmeij@petaltail ~]$ mapDamage --version
+.0.6
+</code>
@@ Line 2881: / Line 3036: @@
   * https://edwards.sdsu.edu/research/c11-on-centos-6/
     * C11++ on CentOS6, two version of gcc
-    * read the R-3.6.1_configure file in ''/share/apps/src/cottontail2''
+    * read the R-3.6.1_configure file in ''/share/apps/CENTOS6/R/R-3.6.1_configure''
 <code>

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