Fixing out of memory Issues in Rsync

If you are doing rsync and you encountered this error like rsync out of memory, you may want to take a look.a this article (Rsync out of memory? Try this…). Need to add an additional parameter (–no-inc-recursive) to the rsync commands.

According to the article, the the out of memory failure occured when  rsync attempts to load all the filenames and info in to RAM at startup.

# rsync -lH -rva --no-inc-recursive --progress gromacs remote_server:/usr/local
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Compiling VASP-5.4.4 with Intel MPI-5.0.3

Details Information can be taken from Installing VASP from VASPwiki. This for CPU Compilation

Activate the Intel Compilers/ Intel MPI Environment. In your .bashrc

source /usr/local/intel_2015/parallel_studio_xe_2015/bin/psxevars.sh intel64
source /usr/local/intel_2015/impi/5.0.3.049/bin64/mpivars.sh intel64
source /usr/local/intel_2015/composerxe/bin/compilervars.sh intel64
source /usr/local/intel_2015/mkl/bin/mklvars.sh intel64
MKLROOT=/usr/local/intel_2015/mkl

At the installation base of vasp.5.4.4 base

# cp arch/makefile.include.linux_intel ./makefile.include

For Linking against Intel-MPI Libraries. Edit makefile.include.linux_intel

# vim makefile.include.linux_intel
MKL_PATH = $(MKLROOT)/lib/intel64
BLACS = -lmkl_blacs_intelmpi_lp64
SCALAPACK = $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)
LLIBS = $(SCALAPACK) $(LAPACK) $(BLAS)

For Linking Intel MKL Wrapper of fftw at makefile.include.linux_intel

OBJECTS= fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o \
         $(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a
INCS=-I$(MKLROOT)/include/fftw

Make the files

# make all

If you wish to build the standard, gamma, non-collinear individually, you should make as below

# make std
# make gam
# make ncl

The vasp binary of standard, gamma-only, and non-collinear version of VASP can be found in the bin folder of vasp

vasp_gam vasp_ncl vasp_std

Making ISO using mkisofs

mkisofs is a wonderful utility to generate ISO images. To generate a compatible ISO images on a disc which are readable everywhere, consider the following commands

# mkisofs -rdlJ -o disc_directory_image.iso directory/

-r : “Rock Ridge” format is enabled to allow long filenames on UNIX systems
-J : allow long filenames on Windows Systems
-l : Allow full 31-character filenames.
-d : Do not append a period to files that do not have one which violate ISO9660

Dealing with The compiler /usr/bin/c++ has no C++11 support for CentOS 6

If you compiling using cmake and you make encounter error like this. This is despite the fact that you use the latest compiler like GNU-5.2.0. But somehow the cmake is still looking at the older gnu that comes with CentOS 6

[user1@node1 build]$ cmake ..
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
CMake Error at CMakeLists.txt:24 (message):
The compiler /usr/bin/c++ has no C++11 support. Aborting.

To resolve this, you have to be more explicit in the cmake parameter point to the corrcet g++, gcc

[user1@node1 build]$ cmake .. -DCMAKE_CXX_COMPILER=/usr/local/gcc-5.2.0/bin/g++ -DCMAKE_C_COMPILER=/usr/local/gcc-5.2.0/bin/gcc