Some of your MATLAB application may require more Java Heap Memory than the default. You may want to edit your ~/.matlab/R2017a/matlab.prf. If you do not have it, just create the file
1. Create matlab.prf
$ touch ~/.matlab/R2017a/matlab.prf2. Increase memory to 36GB
$ vim ~/.matlab/R2017a/matlab.prfJavaMemHeapMax=I36532References:
1. Install Python-34 Numpy, Scipy
# yum -y install python34-numpy
# yum -y install scipy
2. Use Python-3.4 and use “Pip install” to install
# pip install numpy scipy
# pip install -U scikit-learn[alldeps]
3. Test scikit-learn
>>> import sklearn
If you are compiling CentOS 6, you will notice that the R source will not compile without a updated version of zlib, pcre, bzip2. libcurl. There is a very good site on how to compile R on Red Hat Linux
Step 1: Compile R-3.4.2
Download R-3.4.2 from The R Project for Statistical Computing
$ tar -zxvf R-3.4.2.tar.gz
$ ./configure --prefix=/usr/local/RH6_apps/R-3.4.2During configuring…. error surfaced.
checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are requiredStep 2: Compile zlib 1.2.11
a. In your .bashrc
export CFLAGS="-I/usr/local/zlib-1.2.11/include"
export LDFLAGS="-L/usr/local/zlib-1.2.11/lib"b. Compile zlib-1.2.11
$ wget http://zlib.net/zlib-1.2.11.tar.gz
$ tar -zxvf zlib-1.2.11
$ cd zlib-1.2.11
$ configure --prefix=/usr/local/zlib-1.2.11Step 3: Compile bzip2
a. Download the bzip2
$ wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
$ tar xzvf bzip2-1.0.6.tar.gz
$ cd bzip2-1.0.6b. Compile bzip2
$ make -f Makefile-libbz2_so
$ make clean
$ make -n install PREFIX=/usr/local/R-3.4.2
$ make install PREFIX=/usr/local/R-3.4.2Step 4: Compile liblzma or xz
$ wget http://tukaani.org/xz/xz-5.2.3.tar.gz --no-check-certificate
$ tar xzvf xz-5.2.3.tar.gz
$ cd xz-5.2.3
$ ./configure --prefix=/usr/local/xz-5.2.3
$ make -j8
$ make installStep 5: Compile pcre-8.40
$ wget ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.40.tar.gz
$ tar xzvf pcre-8.40.tar.gz
$ ./configure --prefix=/usr/local/pcre-8.40
$ make -j 8
$ make installStep 6: Compile libcurl-7.47.1
$ wget https://curl.haxx.se/download/curl-7.47.1.tar.gz --no-check-certificate
$ tar xzvf curl-7.47.1.tar.gz
$ cd curl-7.47.1
$ ./configure --prefix=/usr/local/curl-7.47.1
$ make -j 8
$ make installStep 7: Update CFLAGS and LDFLAGS
export CFLAGS="-I/usr/local/zlib-1.2.11/include -I/usr/local/bzip2-1.0.6/include -I/usr/local/xz-5.2.3/include -I/usr/local/pcre-8.40/include -I/usr/local/curl-7.47.1/include/curl"
export LDFLAGS="-L/usr/local/zlib-1.2.11/lib -L/usr/local/bzip2-1.0.6/lib -L/usr/local/xz-5.2.3/lib -L/usr/local/pcre-8.40/lib -L/usr/local/curl-7.47.1/lib"Step 8: Compile R-3.4.2
$ ./configure --enable-utf8 --prefix=/usr/local/R-3.4.2
$ make -j 8
$ make installReferences:
Compiling Wannier90-2.1.0 is quite straight-forward.
Step 1: Download the source code from Wannier.Org at http://www.wannier.org/download.html
Step 2: Untar the tar-ball
$ tar -zxvf wannier90-2.1.0.tar.gz
Step 3: Copy and Edit the make file
$ cd wannier90-2.1.0/config $ cp make.inc.ifort .. $ cd .. $ mv make.inc.ifort make.inc
#===================================================== # For Linux with intel version 11/12 on 64bit machines #===================================================== F90 = ifort COMMS=mpi MPIF90=mpiifort FCOPTS=-O2 LDOPTS=-O2 #======================================================== # Intel mkl libraries. Set LIBPATH if not in default path #======================================================== LIBDIR = /usr/local/RH6_apps/intel/mkl/lib/intel64 LIBS = -L$(LIBDIR) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential -lpthread #======================= # ATLAS Blas and LAPACK #======================= #LIBDIR = /usr/local/lib #LIBS = -L$(LIBDIR) -llapack -lf77blas -lcblas -latlas
$ make default -j 8 $ make lib $ make w90chk2chk $ make w90vdw $ make w90pov $ make test $ make doc
IF you need to restart the compilation, you use the command
$ make veryclean
For more information, do take a look at
Taken from VTST.Tools Installation Guide
The VTST•Tools has a fortran component which can be linked into the VASP code as well as a collection of scripts. Its CINEB has some improvement compared to the NEB method
Step 1: Download the VTST Code
Download the VTST Code (vtstcode.tgz) at http://theory.cm.utexas.edu/vtsttools/download.html
Step 2: Download the files in vtsttools/source into your vasp source directory.
In my situation, I put it in /home/user1/vasp.5.3.5_impi_neb/vasp.5.3/
$ tar -zxvf vtstcode.gz $ cd vtstcode-173
$ cp *.* ..
(Replace the chain.F with the new one)
Step 3: Edit main.F in the source file
Find and Replace
CALL CHAIN_FORCE(T_INFO%NIONS,DYN%POSION,TOTEN,TIFOR, & LATT_CUR%A,LATT_CUR%B,IO%IU6)
with
CALL CHAIN_FORCE(T_INFO%NIONS,DYN%POSION,TOTEN,TIFOR, & TSIF,LATT_CUR%A,LATT_CUR%B,IO%IU6)
Step 4: Edit the Makefile
To build the code, the VASP makefile needs to be changed. Find the variable SOURCE, which defines which objects will be built, and add the following objects before chain.o
bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o fire.o lanczos.o neb.o qm.o opt.o \
Step 5: Change and compile the Makefile
Please follow Compiling VASP-5.2.12 with Intel MPI-5.0.3
References:
Installing OpenCV using CentOS 6 using yum is very straightforward. For CentOS 6,
# yum install python-devel python-nose python-setuptools gcc gcc-gfortran gcc-c++ blas-devel lapack-devel atlas-devel
# yum install opencv
Step 1: Create a file to mlm.opt
Step 2: Edit your license.dat file
SERVER myMATLABLicense 00000000000000009
DAEMON MLM "/usr/local/MATLAB/R2016b/etc/MLM" port=1708 options="/usr/local/MATLAB/R2016b/etc/mlm.opt"
.....
.....Step 3: Prepare mlm.opt
# Make user names and host names case insensitive when
# listed in a GROUP or HOST_GROUP. This is not
# required but it is here to prevent some common errors.
GROUPCASEINSENSITIVE ON
# Define GROUP Users
GROUP MATLAB_BLOCK_USERS user1 user2 user3
GROUP MATLAB_INC_USERS user4 user5 user6
# EXCLUDE Users from MATLAB and selected Toolboxes
EXCLUDE "MATLAB asset_info=111111" GROUP MATLAB_BLOCK_USERS
EXCLUDE "Image_Toolbox asset_info=111111" GROUP MATLAB_BLOCK_USERS
EXCLUDE "Signal_Toolbox asset_info=111111" GROUP MATLAB_BLOCK_USERS
# RESERVE for selected for user1
RESERVE 1 "SIMULINK asset_info=111111" USER user1
# Restrict the number of licenses that can be used on machine "server1"
MAX 4 "MATLAB asset_info=111111" HOST server1
# To exclude ALL features
EXCLUDEALL GROUP MATLAB_BLOCK_USERS
#Includes a user or pre-defined group of users, etc.
#Anyone not in an INCLUDEALL statement is not allowed to use these features.
INCLUDEALL GROUP MATLAB_INC_USERS
References:
Here is a write-up of my computing platform and applications:
Step 1: First thing first, source the intel components setting from
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
Step 2: Assuming you are done, you may want to download the NWChem 6.6 from NWChem Website. You may also want to take a look at instruction set for Compiling NWChem.
I have less problem running NWCHEM when the installation and the compiling directories are the same. If you recompile, do untar from source. Somehow the “make clean” does not clean the directories properly.
# tar -zxvf Nwchem-6.6.revision27746-src.2015-10-20.tar.gz # cd nwchem-6.6
Step 3: Apply All the Patches for the 27746 revision of NWChem 6.6
cd $NWCHEM_TOP wget http://www.nwchem-sw.org/download.php?f=Xccvs98.patch.gz gzip -d Xccvs98.patch.gz patch -p0 < Xccvs98.patch
Here is my nwchem_script_Feb2017.sh. For more details information, see Compiling NWChem for details on some of the parameters
export TCGRSH=/usr/bin/ssh export NWCHEM_TOP=/home/melvin/Downloads/nwchem-6.6 export NWCHEM_TARGET=LINUX64 export NWCHEM_MODULES=all export LARGE_FILES=TRUE export ARMCI_NETWORK=OPENIB export IB_INCLUDE=/usr/include export IB_LIB=/usr/lib64 export IB_LIB_NAME="-libumad -libverbs -lpthread" export MSG_COMMS=MPI export USE_MPI=y export USE_MPIF=y export USE_MPIF4=y export MPI_LOC=/usr/local/RH6_apps/intel_2015/impi_5.0.3/intel64 export MPI_LIB=$MPI_LOC/lib export MPI_INCLUDE=$MPI_LOC/include export LIBMPI="-lmpigf -lmpigi -lmpi_ilp64 -lmpi" export FC=ifort export CC=icc export MKLLIB=/usr/local/RH6_apps/intel_2015/mkl/lib/intel64 export MKLINC=/usr/local/RH6_apps/intel_2015/mkl/include export PYTHONHOME=/usr export PYTHONVERSION=2.6 export USE_PYTHON64=y export PYTHONLIBTYPE=so sed -i 's/libpython$(PYTHONVERSION).a/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)/g' config/makefile.h export HAS_BLAS=yes export BLAS_SIZE=8 export BLASOPT="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm" export LAPACK_LIBS="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm" export SCALAPACK_SIZE=8 export SCALAPACK="-L$MKLLIB -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_ilp64 -lpthread -lm" export USE_64TO32=y echo "cd $NWCHEM_TOP/src" cd $NWCHEM_TOP/src echo "BEGIN --- make realclean " make realclean echo "END --- make realclean " echo "BEGIN --- make nwchem_config " make nwchem_config echo "END --- make nwchem_config " echo "BEGIN --- make" make CC=icc FC=ifort FOPTIMIZE=-O3 -j4 echo "END --- make " cd $NWCHEM_TOP/src/util make CC=icc FC=ifort FOPTIMIZE=-O3 version make CC=icc FC=ifort FOPTIMIZE=-O3 cd $NWCHEM_TOP/src make CC=icc FC=ifort FOPTIMIZE=-O3 link
General Site Installation
Determine the local storage path for the install files. (e.g., /usr/local/NWChem).
Make directories
# mkdir /usr/local/nwchem-6.6 # mkdir /usr/local/nwchem-6.6/bin # mkdir /usr/local/nwchem-6.6/data
Copy binary
# cp $NWCHEM_TOP/bin/ /usr/local/nwchem-6.6/bin # cd /usr/local/nwchem-6.6/bin # chmod 755 nwchem
Copy libraries
# cd $NWCHEM_TOP/src/basis # cp -r libraries /usr/local/nwchem-6.6/data # cd $NWCHEM_TOP/src/ # cp -r data /usr/local/nwchem-6.6 # cd $NWCHEM_TOP/src/nwpw # cp -r libraryps /usr/local/nwchem-6.6/data
The Final Lap (From Compiling NWChem)
Each user will need a .nwchemrc file to point to these default data files. A global one could be put in /usr/local/nwchem-6.6/data and a symbolic link made in each users $HOME directory is probably the best plan for new installs. Users would have to issue the following command prior to using NWChem: ln -s /usr/local/nwchem-6.6/data/default.nwchemrc $HOME/.nwchemrc
Contents of the default.nwchemrc file based on the above information should be:
nwchem_basis_library /usr/local/nwchem-6.6/data/libraries/ nwchem_nwpw_library /usr/local/nwchem-6.6/data/libraryps/ ffield amber amber_1 /usr/local/nwchem-6.6/data/amber_s/ amber_2 /usr/local/nwchem-6.6/data/amber_q/ amber_3 /usr/local/nwchem-6.6/data/amber_x/ amber_4 /usr/local/nwchem-6.6/data/amber_u/ spce /usr/local/nwchem-6.6/data/solvents/spce.rst charmm_s /usr/local/nwchem-6.6/data/charmm_s/ charmm_x /usr/local/nwchem-6.6/data/charmm_x/
References:
Compile swig-3.0.12
Do download http://www.swig.org/index.php.
PCRE needs to be installed on your system to build SWIG, in particular pcre-config must be available. For more information on SWIG installation do take a look at http://www.swig.org/Doc3.0/SWIGDocumentation.html
./configure --prefix=/usr/local/RH6_apps/swig-3.0.12 --with-pcre-prefix=/usr/local/RH6_apps/pcre-8.40 --without-clisp --without-maximum-compile-warnings # make # make install
The Linux Cluster 