Compiling HDF5-1.8.17 with Intel-15.0.6 and Intel-MPI-5.0.6

Step 1: Preparing the prerequisites

$ vim .bashrc

source /usr/local/intel_2015/bin/compilervars.sh intel64
source /usr/local/intel_2015/impi/5.0.3.049/bin64/mpivars.sh intel64
source /usr/local/intel_2015/mkl/bin/mklvars.sh intel64
export CC=icc
export CXX=icpc
export F77=ifort
export MPICC=mpicc
export MPICXX=mpiicpc
export CFLAGS="-O3 -xHost -fno-alias -align"
export FFLAGS="-O3 -xHost -fno-alias -align"
export CXXFLAGS="-O3 -xHost -fno-alias -align"
export FFlags="-I/usr/local/intel_2015/impi/5.0.3.049/include64 -L/usr/local/intel_2015/impi/5.0.3.049/lib64"

Step 2: Compile zlib-1 See Compile zlib-1.2.8 with Intel-15.0.6 Step 3: Configure the HDF5

$ tar -zxvf hdf5-1.8.17.tar.gz
$ cd hdf5-1.8.17
$ ./configure --prefix=/usr/local/hdf5-1.8.17 --enable-fortran --enable-cxx
$ make
$ make check
$ make install

References

1. Building HDF5* with Intel® compilers
2. Obtaining The Latest HDF5 Software

Compile zlib-1.2.8 with Intel-15.0.6

Step 1: Download the zlib from HDF5 (https://support.hdfgroup.org/HDF5/release/obtain5.html)

In your .bashrc, you can

source /usr/local/intel_2015/bin/compilervars.sh intel64
source /usr/local/intel_2015/impi/5.0.3.049/bin64/mpivars.sh intel64
source /usr/local/intel_2015/mkl/bin/mklvars.sh intel64
export CC=icc
export CFLAGS='-O3 -xHost -ip'

At your command prompt,

$ tar -zxvf zlib-1.2.8.tar.gz
$ cd zlib-1.2.8
$ ./configure --prefix=/usr/local/zlib-1.2.7
$ make
$ make check
$ make install

References:

1. Building HDF5* with Intel® compilers

Python-yaml Libraries for Python 3

If you are searching for Python-yaml and not able to locate the libraries, you might want to try

# ./pip search yaml

You should see something like pyyaml

# ./pip install -upgrade  pyyaml

X Unable to launch

I was trying to launch X Windows after yum install  yum groupinstall "Desktop" "Desktop Platform" "General Purpose Desktop"

 But I was not able to launch X. Instead I got

Fatal server error:
[ 9491.484] could not open default font 'fixed'
[ 9491.484] (EE)
Please consult the CentOS support
at http://wiki.centos.org/Documentation
for help. (done)
[ 9491.484] (EE) Please also check the log file at "/var/log/Xorg.0.log" for additional information.

To solve this,

# yum -y install libXfont

Ctrl-C caught... cleaning up processes

We were submitting a NAMD Job and we have an error logs as well as

"Ctrl-C caught... cleaning up processes"

To solve the issues,  you may want to first decide to whether there are Windows Format traces in the input files

$ dos2unix inputfile

[mpiexec@comp175] HYD_pmcd_pmiserv_send_signal (./pm/pmiserv/pmiserv_cb.c:239): assert (!closed) failed
[mpiexec@comp175] ui_cmd_cb (./pm/pmiserv/pmiserv_pmci.c:127): unable to send SIGUSR1 downstream
[mpiexec@comp175] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status
[mpiexec@comp175] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:435): error waiting for event
[mpiexec@comp175] main (./ui/mpich/mpiexec.c:901): process manager error waiting for completion

NetApp and OpenStack

1. NetApp OpenStack site
https://netapp.github.io/openstack/

2. Continuous Operations with OpenStack’s File-Share Service (Manila)
https://www.youtube.com/watch?v=Mvhx1gRgUUI

3. NetApp - Jumpstart Your Production OpenStack
https://www.youtube.com/watch?v=5YZPHc2y7XY

More Information on Charm++ and NAMD

Information / Scripts for NAMD

1. Running NAMD - Linux or Other Unix Workstation Networks
2. Components of a Charm++ Program