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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Ports used by PBS Analytics

The default http port for the PBSA service is 9000.
The default https port for the PBSA service is 9143.
The default https port for the PBSA data collector is 9343.
The default port for the PBSA MonetDB is 9200.
The default port for the Envision Tomcat-8 server is 9080.
The default https port for Envision is 9443
The default port for the PBSA MongoDB is 9700.

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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/