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Compiling OpenFOAM-5.0 with Intel-MPI

Minimum Requirements version

  1. gcc: 4.8.5
  2. cmake: 3.3 (required for ParaView and CGAL build)
  3. boost: 1.48 (required for CGAL build)
  4. fftw: 3.3.7 (optional – required for FFT-related functionality)
  5. Qt: 4.8 (optional – required for ParaView build)

I’m using Intel-16.0.4 and Intel-MPI-5.1.3.258

Step 1a: Download and Unpacking Sources

# wget -O - http://dl.openfoam.org/source/5-0 | tar xvz
# wget -O - http://dl.openfoam.org/third-party/5-0 | tar xvz

Step 1b:  Rename the Directory

# mv OpenFOAM-5.x-version-5.0 OpenFOAM-5.0
# mv ThirdParty-5.x-version-5.0 ThirdParty-5.0

Step 2: Initiate Intel and Intel-MPI Environment and source OpenFOAM-5.0 bashrc

source /usr/local/intel/bin/compilervars.sh intel64
source /usr/local/intel/parallel_studio_xe_2016.4.072/bin/psxevars.sh intel64
source /usr/local/intel/impi/5.1.3.258/bin64/mpivars.sh intel64
source /usr/local/intel/mkl/bin/mklvars.sh intel64
source /usr/local/OpenFOAM/OpenFOAM-5.0/etc/bashrc
export MPI_ROOT=/usr/local/intel/impi/5.1.3.258/intel64

Step 3: Make sure your CentOS-7 Environment have the following base packages

# yum install gcc-c++ gcc-gfortran gmp flex flex-devel boost zlib zlib-devel qt4 qt4-devel

Step 4: Edit the OpenFOAM  internal bashrc

# vim /usr/local/OpenFOAM/OpenFOAM-5.0/etc/bashrc

Line 35,36

export WM_PROJECT=OpenFOAM
export WM_PROJECT_VERSION=5.0

Line 45

FOAM_INST_DIR=/usr/local/$WM_PROJECT

Line 60

export WM_COMPILER_TYPE=system

Line 65

export WM_COMPILER=Icc

Line 88

export WM_MPLIB=INTELMPI

Step 5: Compile OpenFOAM

# ./Allwmake -update -j
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Faulty disks accepting I/O request and not returning any failure for GPFS

We have encountered a situation where a defunct disk was accepting IO request and did not return any failure in time. As a result, these IO requests hanged there till time out (default 10 seconds). Typically, Spectrum Scale/GPFS will fail to read or write a disk, the failure is written in log and we have to shift IO to other available disks which should be quick.

Normally such operations should return in 20 milliseconds or less. When we have IO timeout, this request has wasted us
10 seconds / 20 milliseconds = 500 times of time. Even if Spectrum Scale/GPFS is able to choose a fast disk in the second attempt, we are much slower than normal.

Due to the utilization of striping technology, a bad/slow disks always affects IO of many files, much more than the situation without striping. IO on the same file involves more than several disks, and the IO has to wait for the slowest request to return. So a bad/slow disk may have considerable influence on Spectrum Scale/GPFS performance.

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“The command gnome-session existed with signal 15” on CentOS 7 for FastX2

If you have an error message when you launched FastX2 client, you will see this error “The command gnome-session existed with signal 15” on CentOS 7 for FastX2.

Step 1: This error is caused by selinux on CentOS 7. Do the following /etc/selinux

SELINUX=disabled

Trying to use the command “setenforce 0” does not seems to be able to fix the issue.

Step 2: Remember to install GNOME Desktop

# yum groupinstall "GNOME Desktop" "Graphical Administration Tools"

Step 3: Uninstall the StarNetFastX2 and reinstall

# rpm -e StarNetFastX2
# rpm -Uvh --force StarNetFastX2-2.4.7.rhel6.x86_64.rpm
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Disable FirewallD Services on CentOS 7

Do note that firewall on CentOS 7 system is enabled by default.

Step 1: To check the status of CentOS 7 FirewallD

# systemctl status firewalld.service
● firewalld.service - firewalld - dynamic firewall daemon
   Loaded: loaded (/usr/lib/systemd/system/firewalld.service; disabled; vendor preset: enabled)
   Active: inactive (dead)
     Docs: man:firewalld(1)

The above shows that the firewalld is disabled.

Step 2: To stop the FirewallD

# systemctl stop firewalld.service

Step 3: To completely disable the firewalld service

# systemctl disable firewalld.service
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Resolving “lsb_release not found” on CentOS 7

I was installing ABAQUS 2017 on CentOS 7 when I encountered an error. lsb_release is the print distribution specific information. Strangely, this issue is found on CentOS 7 distribution.

[root@node-h001 1]# ./StartGUI.sh
CurrentMediaDir initial="."
CurrentMediaDir="/root/abaqus2017/AM_SIM_Abaqus_Extend.AllOS/1"
Current operating system: "Linux"
./StartGUI.sh[21]: .[31]: .: line 3: lsb_release: not found
DSY_OS_Release=""
Unknown linux release ""
exit 8

Resolving Issues

# yum install redhat-lsb-core

Verification

[root@node-h001 1]# lsb_release
LSB Version: :core-4.1-amd64:core-4.1-noarch