Tuesday, August 23, 2016

Installing NAMD 2.9 with Intel Cluster Studio 2013 with IB support

There is a very good article of Installing NAMD 2.9 with Intel Cluster Studio 2013 with IB support. You may want to take a look at

Saturday, August 20, 2016

List of mkl_solver* libraries are deprecated libraries since version 10.2 Update 2

Taken from mkl_solver* libraries are deprecated libraries since version 10.2 Update 2

Since version 10.2 update 2 of Intel® MKL,
all components of Direct Solver (Pardiso and DSS), Trust-Region (TR) Solver, Iterative Sparse Solver (ISS) and GNU Multiple Precision (GMP) were moved to standard MKL libraries.
So now solver ( e.g: mkl_solver.lib and mkl_solver_sequential.lib for IA32 ) libraries are
empty (for backward compatibility).
The list of deprecated libraries are the following:

Intel® MKL for Linux:


Therefore, the updated linking line will look like:

Linking on Intel®64:
static linking:
ifort pardiso.f -L$MKLPATH -I$MKLINCLUDE \
-Wl,--start-group \
$MKLPATH/libmkl_intel_lp64.a $MKLPATH/libmkl_intel_thread.a $MKLPATH/libmkl_core.a \
-Wl,--end-group -liomp5 -lpthread
dynamic linking:
ifort pardiso.f -L$MKLPATH -I$MKLINCLUDE \
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread
In these examples,

Thursday, August 18, 2016

Compiling CPMD-3.17.1 with Intel- and OpenMPI-1.8.3

I’m assuming you have compiled OpenMPI with Intel Compiler. If you are not sure, you can look at Blog Entry
Compiling OpenMPI 1.6.5 with Intel 12.1.5 on CentOS 6
To get the source code from CPMD, please go to http://www.cpmd.org/

Step 1: From the CPMD Directory
cd ~/CPMD-3.13.2/SOURCE
./mkconfig.sh IFORT-AMD64-MPI > Makefile

Step 2: I’m using CentOS 6 internal Blas, lapack and atlas. Make sure your configure the one below.
#--------------- Default Configuration for IFORT-AMD64-MPI ---------------
SRC  = .
DEST = .
BIN  = .
FFLAGS = -pc64  -tpp6 -O2 -unroll
#LFLAGS =  -L. -latlas_x86_64
LFLAGS =  -L/usr/lib64/atlas -llapack -lblas
CFLAGS = -O2 -Wall -m64
CPP = /lib/cpp -P -C -traditional
CC = mpicc
FC = mpif77 -c
LD = mpif77 -i-static
AR = ar

Step 3: Compile CPMD
# make
If the compilation succeed, it should generate a cpmd.x executable.

Step 4: Pathing
Make sure your $PATH reflect the path of the executable cpmd.x. It is also important to ensure that you check that the libraries are properly linked to the executable
# ldd cpmd.x

Step 5: Test your executable. You have to go to CPMD Consortium to download the cpmd-test.tar.gz for testing.

I/O Direction for Bash

This is a good article on I/O Redirection. I have always been interest to redirect stderr to stdout. So here is it 2>&1

      # Redirects stderr to stdout.
      # Error messages get sent to same place as standard output.
        >>filename 2>&1
            bad_command >>filename 2>&1
            # Appends both stdout and stderr to the file "filename" ...
        2>&1 | [command(s)]
            bad_command 2>&1 | awk '{print $5}'   # found
            # Sends stderr through a pipe.
            # |& was added to Bash 4 as an abbreviation for 2>&1 |.

Tuesday, August 16, 2016

Enable Centrify Agent to read UID and GID from Centrify DirectManage Access Manager

We purchased Centrify Standard and setup the DirectManage Access Manager. Next we proceed to install the client agent on the compute node.

After unpacking and installing the agent, when we do a
# getent passwd  |grep kittycool

Apparently, the getent passwd |grep kittycool is pulling both the Active Directory UID and the DirectManage Access and the user UID differs

To resolve this issue, you need to specify the zone which is used by DirectManage Access Manager, so your UID of the user will pick from the DirectManage Access Manager.
# adjoin -z cluster -u OU_Administrator  staff.mycompany.com.sg -c "staff.mycompany.com.sg/HPC/Computers"

To check it is displaying the correct UID and GID,
# getent passwd  |grep kittycool