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--- cluster:73 [2023/04/26 20:20]
hmeij07 [LAMMPS CPU/GPU]
+++ cluster:73 [2023/10/31 14:16]
hmeij07 [Miniconda3-py311]
@@ Line 25: / Line 25: @@
+====== Miniconda3-py311 ======
+  * Starting a new branch, the other Miniconda3 section listed on this is quite loaded
+  * Python 3.11
+<code>
+source /share/apps/CENTOS7/miniconda3-py311/etc/profile.d/conda.sh
+or
+export PATH=/share/apps/CENTOS7/miniconda3-py311/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/miniconda3-py311/lib:$LD_LIBRARY_PATH
+which mpirun python conda
+conda list
+export CUDA_HOME=/usr/local/cuda
+export PATH=/usr/local/cuda/bin:$PATH
+export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
+</code>
+  * conda install (same as what is listed on openhpc [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:215#miniconda3-py311|miniconda3-py311]]) page
+  * cudatoolkit=10.2 cudnn=7 for exx96 queue
+  * same error, module cudatoolkit not found, but I found Cupy and it does load
+  * https://docs.cupy.dev/en/stable/overview.html
+  * thayerlab
+<code>
+# pollacklab
+[hmeij@greentail52 ~]$ source /share/apps/CENTOS7/miniconda3-py311/etc/profile.d/conda.sh
+[hmeij@greentail52 ~]$ conda activate sage
+(sage) [hmeij@greentail52 ~]$ sage --version
+SageMath version 10.0, Release Date: 2023-05-20
+(sage) [hmeij@greentail52 ~]$ sage
+┌────────────────────────────────────────────────────────────────────┐
+│ SageMath version 10.0, Release Date: 2023-05-20                    │
+│ Using Python 3.11.4. Type "help()" for help.                       │
+└────────────────────────────────────────────────────────────────────┘
+</code>
+====== Masurca ======
+  * module: masurca/4.1.0
+  * https://github.com/alekseyzimin/masurca/releases
+  * supports openmp (maybe)
+  * queues mwgpu, exx96 (centos 7)
+<code>
+export PATH=/share/apps/CENTOS7/masurca/4.1.0/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/masurca/4.1.0/lib:$LD_LIBRARY_PATH
+[hmeij@cottontail2 ~]$ masurca --version
+version 4.1.0
+</code>
 ====== Trimmomatic ======
@@ Line 346: / Line 415: @@
 ** Flye **
-Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2)
+Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52.
+  * setup env as for all packages in #3, see top of section
+  * v2.9.2 (June 2023)
+  * python bin/flye
+    * change the PATHS accordingly
+<code>
+/share/apps/CENTOS7/flye/2.9.2/bin/flye --version
+.9.2-b1794
+</code>
   * v2.9.1 (October 2022)
@@ Line 373: / Line 454: @@
 </code>
-  * https://github.com/fenderglass/Flye
-  * miniconda3
-  * De novo assembler for single molecule sequencing reads using repeat graphs
-  * v2.8.3
-<code>
-# To activate this environment, use
-#     $ conda activate flye
-# To deactivate an active environment, use
-#     $ conda deactivate
-</code>
 ** Filtlong **
@@ Line 414: / Line 483: @@
 export LD_LIBRARY_PATH=/share/apps/CENTOS7/bamtools/2.5.2/lib:$LD_LIBRARY_PATH
 ldd `which bamtools`
+</code>
+** BBmap **
+  * location: /share/apps/CENTOS7/bbmap/39.01
+  * java programs
+  * https://sourceforge.net/projects/bbmap/
+** Pilon **
+  * location: /share/apps/CENTOS7/pilon/
+  * just one big jar file
+  * latest java is in $PATH
+<code>
+[hmeij@greentail52 pilon]$ java -jar pilon-1.24.jar --help
+Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
+    Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam]
+                 [...other options...]
+           pilon --help for option details
+<snip>
+</code>
+** haslr **
+  * miniconda3 env
+  * https://github.com/vpc-ccg/haslr
+  * conda install -c bioconda haslr
+<code>
+The following NEW packages will be INSTALLED:
+  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
+  fastutils          bioconda/linux-64::fastutils-0.3-hdcf5f25_4
+  haslr              bioconda/linux-64::haslr-0.8a1-py39hd65a603_4
+  k8                 bioconda/linux-64::k8-0.2.5-hdcf5f25_4
+  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_2
+  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5
+  minia              bioconda/linux-64::minia-3.2.6-hdcf5f25_3
+  minimap2           bioconda/linux-64::minimap2-2.26-he4a0461_1
+  pluggy             conda-forge/noarch::pluggy-1.3.0-pyhd8ed1ab_0
+  ruamel.yaml        conda-forge/linux-64::ruamel.yaml-0.17.32-py39hd1e30aa_0
+  ruamel.yaml.clib   conda-forge/linux-64::ruamel.yaml.clib-0.2.7-py39h72bdee0_1
+  toolz              conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0
+</code>
+Compiled from source, do **not** source miniconda3, we are using standalone pyhton3
+<code>
+export PATH=/share/apps/CENTOS7/gcc/9.2.0/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/9.2.0/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/9.2.0/lib:$LD_LIBRARY_PATH
+export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
+[hmeij@greentail52 20231006]$ which python
+/share/apps/CENTOS7/python/3.8.3/bin/python
+[hmeij@greentail52 20231006]$ pwd
+/share/apps/CENTOS7/haslr/20231006
+[hmeij@greentail52 20231006]$ ll bin
+total 11448
+-rwxr-xr-x 1 hmeij its   123448 Oct  6 15:01 fastutils
+-rwxr-xr-x 1 hmeij its  3823032 Oct  6 15:04 haslr_assemble
+-rwxr-xr-x 1 hmeij its    19949 Oct  6 14:48 haslr.py
+-rwxr-xr-x 1 hmeij its 20969840 Oct  6 14:59 minia
+-rwxr-xr-x 1 hmeij its    23856 Oct  6 15:01 minia_nooverlap
+-rwxr-xr-x 1 hmeij its   951922 Oct  6 14:59 minimap2
+</code>
+** stLFR **
+  * same centos 7 environment
+  * https://github.com/BGI-Qingdao/stLFR_GapCloser
+<code>
+cd /share/apps/CENTOS7/stLFR/20230929
+[hmeij@greentail52 20230929]$ ./Release/stLFR_GapCloser -h
+Version:
+.00
+Contact:
+	dengli1@genomics.cn && guolidong@genomics.cn
+Usage:
+	stLFR_GapCloser [options]
+...
+# and another request by Luis
+# https://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2
+[hmeij@greentail52 stLFR]$ pwd
+/share/apps/CENTOS7/stLFR
+[hmeij@greentail52 stLFR]$ ll GapCloser-bin-v1.12-r6/
+total 175
+-rwxr-xr-x 1 hmeij its 184713 Jan 11  2013 GapCloser
+-rw-r--r-- 1 hmeij its  44533 Jan 11  2013 GapCloser_Manual.pdf
+</code>
+** BUSCO **
+  * https://busco.ezlab.org/busco_userguide.html#docker-image
+  * conda package fails on glib 2.17, weird
+<code>
+[hmeij@n79 ~]$ docker images
+REPOSITORY                         TAG                            IMAGE ID            CREATED             SIZE
+ezlabgva/busco                     v5.5.0_cv1                     30d3e831aba7        2 months ago        2.88GB
+[hmeij@n79 busco_wd]$ docker run --rm -v $(pwd):/busco_wd -u $(id -u):$(id -g) ezlabgva/busco:v5.5.0_cv1 busco -i /busco_wd/assembly.fasta -l actinopterygii_odb10 -o Busco_Output -m geno -f
+-10-28 20:30:00 INFO:       ***** Start a BUSCO v5.5.0 analysis, current time: 10/28/2023 20:30:00 *****
+-10-28 20:30:00 INFO:       Configuring BUSCO with local environment
+-10-28 20:30:00 INFO:       Mode is genome
+-10-28 20:30:00 INFO:       'Force' option selected; overwriting previous results directory
+-10-28 20:30:00 INFO:       Downloading information on latest versions of BUSCO data...
+that's a problem, trying to reach the internet ...
 </code>
@@ Line 719: / Line 920: @@
 fasteners-0.18 mmtf-python-1.1.3
 mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4
+</code>
+For **Lammps** (starrlab) 23April2023, consult install file
+  *  /share/apps/CENTOS7/lammps/25Apr2023.install
+  * make yes-ml-pace
+  * make yes-gpu
+  * https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
+<code>
+# Note: you must add this line to you env
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/pkgs/cudatoolkit-11.0.221-h6bb024c_0/lib:$LD_LIBRARY_PATH
+# Note2: had to install 'conda install cudnn' and make two links
+to higher level libraries (a must not do)
+for libcudnn.so.8 and libcusolver.so.11
+[hmeij@greentail52 ~]$ which python
+/share/apps/CENTOS7/amber/miniconda3/bin/python
+[hmeij@greentail52 ~]$ pip list | grep tensorflow
+mesh-tensorflow              0.1.19
+tensorflow                   2.8.0
+tensorflow-addons            0.15.0
+tensorflow-datasets          4.4.0
+tensorflow-estimator         2.7.0
+tensorflow-gan               2.1.0
+tensorflow-hub               0.12.0
+tensorflow-io-gcs-filesystem 0.32.0
+tensorflow-metadata          1.4.0
+tensorflow-probability       0.15.0
+[hmeij@greentail52 ~]$ which pacemaker
+/usr/bin/which: no pacemaker in (...failed to install at first, see readme install file)
 </code>
@@ Line 733: / Line 968: @@
   * git clone https://github.com/Amber-MD/pytraj; cd pytra
   * python ./setup.py install
-  * requires CentOS7 so queues mwgpu, amber128 and exx96
+  * requires CentOS7 so queues mwgpu, <del>amber128</del> and exx96
   * or for debugging use greentail52
   * /share/apps/CENTOS7/amber/pytraj
@@ Line 1058: / Line 1293: @@
 pcangsd --version
 pcangsd 1.10
+</code>
+  * **angsd**, requires miniconda3, same environment as pcangsd
+  * http://www.popgen.dk/angsd/index.php/RealSFS
+  * add location of angsd to PATH env
+<code>
+$ pwd
+/share/apps/CENTOS7/angsd/0.940/angsd
+$ ls -l angsd
+-rwxr-xr-x 1 hmeij its 5517248 Jul  6 14:11 angsd
+$ ./angsd
+	-> angsd version: 0.940-dirty (htslib: 1.16) build(Jul  6 2023 14:11:30)
 </code>
@@ Line 2078: / Line 2330: @@
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
+  * program v13,2.1 installed
+  * program v13.2 installed
   * program: mcc, math, mathematica (v 12.2)
@@ Line 2281: / Line 2537: @@
   * lmp_serial and lmp_mpi
   * 3 cuda versions with 3 different precision settings
+  * notes: /share/apps/CENTOS7/lammps/25Apr2023.install
+  * does **not** support openmp, look for the OpenHPC version for that
+  * 05/24/2023 remade with package CREATION added
+  * also read miniconda3 section for tensorflow/pacemaker info
 <code>
@@ Line 2286: / Line 2546: @@
 # CPU
+ export PATH=/share/apps/CENTOS7/gcc/6.5.0/bin/:$PATH
+ export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH
  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
  export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
  export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
- which mpirun mpicc python
+ which mpirun mpicc python gcc
 # CPU + GPU (exx96 queue, may run on test and amber128 queues)
@@ Line 2299: / Line 2562: @@
  export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
  which nvcc
+# related for starrlab
+# https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
+[hmeij@cottontail2 ~]$ module load miniconda3/py39
+[hmeij@cottontail2 ~]$ which pacemaker
+/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/pacemaker
+[hmeij@cottontail2 ~]$ pacemaker --version
+pacemaker/pyace version: 0.2.7+77.g8b40c11
+ace_evaluator   version: 2022.6.27
+[hmeij@cottontail2 ~]$ python
+Python 3.9.10 | packaged by conda-forge | (main, Feb  1 2022, 21:24:11)
+[GCC 9.4.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import pyace as py
+>>>
@@ Line 3792: / Line 4072: @@
 <code>
+# update
+[hmeij@greentail52 ~]$ java --version
+java 20.0.2 2023-07-18
 export JAVAHOME=/home/apps/j2sdk1.4.2_17/bin:$PATH
 export CLASSPATH=$JAVAHOME/lib:$CLASSPATH
@@ Line 4146: / Line 4432: @@
 ====== Matlab ======
+  * installed R2023a
+  * installed R2022a
+  * installed R2021a
   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
@@ Line 4166: / Line 4456: @@
 ====== Stata ======
+  * program stata[-mp|-se] in your $PATH, version 18
+  * v17 will still run so add '17' to the command like 'stata-mp17'
+  * so that makes for 12 licenses 8-)
   * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se

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