Month: October 2019

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IBM Community Compilers for Power

Compiler options:

– GNU Compiler Collection (GCC) for Linux on Power:
https://developer.ibm.com/linuxonpower/2018/06/28/gnu-compiler-collection-gcc-linux-power/

– IBM Advance Toolchain for Linux on Power:
https://developer.ibm.com/linuxonpower/advance-toolchain/

– IBM XL C/C++ for Linux Community Edition:
https://www.ibm.com/us-en/marketplace/xl-cpp-linux-compiler-power

– IBM XL Fortran for Linux Community Edition:
https://www.ibm.com/us-en/marketplace/xl-fortran-linux-compiler-power

Libraries:

– IBM ESSL Community Edition:
https://epwt-www.mybluemix.net/software/support/trial/cst/welcomepage.wss?siteId=589&tabId=1174&w=1

AI platform:

– IBM WML Community Edition:
https://www.ibm.com/support/knowledgecenter/en/SS5SF7_1.6.1/navigation/wmlce_download.html

MPI:

– It can be found at MPI IBM WML Community Conda Channel. It is found at spectrum-mpi for linux-ppc64le.
https://public.dhe.ibm.com/ibmdl/export/pub/software/server/ibm-ai/conda/#/

 

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Testing for license checkout for MATLAB_Distrib_Comp_Engine

If you need to check whether you can check out the distributing computer

[user1@hpc-gekko1 ~]# /usr/local/MATLAB/R2019a/bin/matlab -dmlworker =r "license, exit"
X11 connection rejected because of wrong authentication.
MATLAB is selecting SOFTWARE OPENGL rendering.
======BEGIN LICENSE MANAGER ERROR======
License checkout failed.
License Manager Error -5
Cannot find a license for MATLAB_Distrib_Comp_Engine.
Troubleshoot this issue by visiting:
https://www.mathworks.com/support/lme/R2019a/5

Diagnostic Information:
Feature: MATLAB_Distrib_Comp_Engine
License path: /root/.matlab/R2019a_licenses:/usr/local/MATLAB/R2019a/licenses/license.dat:/usr/local/MATLAB/R2019a
/licenses/network.lic
Licensing error: -5,147. System Error: 2======END LICENSE MANAGER ERROR======

2. Check the “normal MATLAB License Server”

$ /usr/local/MATLAB/R2019a/etc/glnxa64/lmutil lmstat -a -c ../../licenses/network.lic -f MATLAB_Distr_Comp_Engine
lmutil - Copyright (c) 1989-2017 Flexera Software LLC. All Rights Reserved.
Flexible License Manager status on Thu 10/24/2019 12:31

License server status: 27000@xxx.xxx.xxx.xxx
License file(s) on xxx.xxx.xxx.xxx: C:\Program Files\MATLAB\R2019b\etc\license.dat:

xxx.xxx.xxx.xxx: license server UP v11.16.2

Vendor daemon status (on N4SAP0048):

MLM: UP v11.16.2
Feature usage info:
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Compiling STAR 2.7 with Intel Compiler 2018 on CentOS 7

What is STAR 2.7?
Spliced Transcripts Alignment to a Reference
https://www.ncbi.nlm.nih.gov/pubmed/23104886


Hardware/Software Requirements
x86-64 compatible processors


Manual
https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf


Compiling for Source
# Source Intel Compilers

source /usr/local/intel/2018u3/bin/compilervars.sh intel64
source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64
source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64
source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64
MKLROOT=/usr/local/intel/2018u3/mkl
# wget https://github.com/alexdobin/STAR/archive/2.7.1a.tar.gz
# tar -xvzf 2.7.1a.tar.gz
# cd STAR-2.7.1a/source
# mkdir /usr/local/STAR-2.7.1a
# cp STAR /usr/local/STAR-2.7.1a/
# cp STARlong /usr/local/STAR-2.7.1a/
# cp -r htslib /usr/local/STAR-2.7.1a/