CHARMM c41b2

• Installation date: 5/06/2017
• URL: https://www.charmm.org/charmm
• Apolo version: Apolo II
• License: Payment (Special Contract)

Table of contents

• CHARMM c41b2
  • Dependencies
    • Apolo
    • Cronos
  • Installation
    • Apolo
    • Cronos
  • Module
  • Mode of Use
  • SLURM Template
  • References
  • Author

Dependencies

Apolo

• MPICH 3.2 (This must be compiled without using the PMI interface, as there is a bug with SLURM which makes it impossible to run distributed jobs)
• GCC-5.4.0
• Source code GAMESS 2016 R1
• Cmake >= 3.7.1

Cronos

• Gnu GCC >= 5.5.0
• Mpich2 >= 3.2.1
• FFTW3 >= 3.3.7
• CMake >= 3.10.2
• Source code GAMESS 2016 R1 (gamess-current.tar.gz)

Installation

Apolo

After resolving to load the previously mentioned dependencies, you can proceed with the installation of CHARMM-GAMESS.

1. Prepare the environment before compilation:

$ cd /apps/charmm/src/charmm-gammess
$ tar xf c41b2.tar.gz
$ cd charmm
$ wget http://ala.cmm.ki.si/gamess/20160818.1/gamess-20160818.1-charmm.tar.gz
$ tar xf gamess-20160818.1-charmm.tar.gz
$ rm gamess-20160818.1-charmm.tar.gz
$ mkdir source/gamint/gamess
$ cp ~/apps/gamess/src/gamess/source/* source/gamint/gamess/
$ rm source/gamint/gamess/vector.src
$ rm source/gamint/gamess/ga.src
$ module unload slurm/16.05.6
$ module load mpich2/3.2_gcc-5.4.0 cmake/3.7.1
$ patch -p1 < gamess/gamess2016-for-charmm.patch
$ patch -p1 < gamess/c41b2-for-gamess.patch
$ chmod 755 tool/gmscomp

For the moment ignore this step.

We comment on the following line in the tool/gmscomp file:

$ emacs /home/mgomezzul/apps/charmm/src/charmm-gammess/charmm/tool/gmscomp
$ ...
$ #set EXTRAOPT="$EXTRAOPT -w -fno-aggressive-loop-optimizations -fno-sanitize=all"
$ ...

2. After preparing the compilation environment we proceed with the compilation:

$ mkdir -p ~/charmm/build
$ cd ~/charmm/build
$ ~/apps/charmm/src/charmm-gammess/charmm/configure --gamess
$ make -j 8

3. At the end of the execution of the make -j 8, several errors related to functions that are not defined will result, this happens because the CHARMM and GAMESS compilation methods are different, making cmake unable to produce the dependencies for the parallel compilation of the program. This is why it is necessary to apply a new patch and recompile again.

$ cd ~/apps/charmm/src/charmm-gammess/charmm
$ patch -p1 < gamess/c41b2-phase2.patch
$ cd ~/charmm/build
$ make -j 8

4. After finishing with the last parallel make, the charmm binary should have been produced, we can try it as follows:

$ ./charmm
...
1
                Chemistry at HARvard Macromolecular Mechanics
        (CHARMM) - Developmental Version 41b2   February 15, 2017
                            Revision unknown
    Copyright(c) 1984-2014  President and Fellows of Harvard College
                            All Rights Reserved
  Current operating system: Linux-2.6.32-504.16.2.el6.x86_64(x86_64)@deb
              Created on  6/6/17 at  9:36:54 by user: mgomezzul

         Maximum number of ATOMS:    360720, and RESidues:      120240
...

Cronos

After resolving to load the previously mentioned dependencies, you can proceed with the installation of CHARMM-GAMESS.

1. Prepare the compilation environment:

$ cd /home/mgomezzul/apps/charmm-gammes/src/gcc-5.5.0_mpich2-3.2.1
$ tar xf c41b2.tar.gz
$ cd charmm
We download the patch that allows you to compile charmm with support for gamess
$ wget http://ala.cmm.ki.si/gamess/20160818.1/gamess-20160818.1-charmm.tar.gz
$ tar xf gamess-20160818.1-charmm.tar.gz
$ rm gamess-20160818.1-charmm.tar.gz
$ mkdir source/gamint/gamess
$ cp  ~/apps/gammess/src/gamess/source/* source/gamint/gamess/
$ rm source/gamint/gamess/vector.src
$ rm source/gamint/gamess/ga.src
$ module purge
$ module load fftw/3.3.7_gcc-5.5.0_mpich2-3.2.1 cmake/3.10.2
$ patch -p1 < gamess/gamess2016-for-charmm.patch
$ patch -p1 < gamess/c41b2-for-gamess.patch
$ chmod 755 tool/gmscomp

2. The following line is commented in the tool/gmscomp file:

$ emacs /home/mgomezzul/apps/charmm-gammes/src/gcc-5.5.0_mpich2-3.2.1/charmm/tool/gmscomp
$ ...
$ #set EXTRAOPT="$EXTRAOPT -w -fno-aggressive-loop-optimizations -fno-sanitize=all"
$ ...

3. After preparing the compilation environment we proceed with it:

$ mkdir -p ~/apps/charmm-gammes/build
$ cd ~/apps/charmm-gammes/build
$ FFTWDIR=/share/apps/fftw/3.3.7/gcc-5.5.0_mpich2-3.2.1 FFTW_HOME=/share/apps/fftw/3.3.7/gcc-5.5.0_mpich2-3.2.1 ~/apps/charmm-gammes/src/gcc-5.5.0_mpich2-3.2.1/charmm/configure --prefix=/share/apps/charmm/c41b2/gcc-5.5.0_mpich2-3.2.1 --gamess --with-gcc
$ make -j 16 | tee make-charmm.log

4. At the end of the execution of the make -j 16, several errors related to functions that are not defined will result, this happens because the CHARMM and GAMESS compilation methods are different, making cmake unable to produce the dependencies for the parallel compilation of the program. This is why it is necessary to apply a new patch and recompile again.

$ cd /home/$USER/apps/charmm-gammes/src/gcc-5.5.0_mpich2-3.2.1
$ patch -p1 < gamess/c41b2-phase2.patch
$ cd /home/$USER/apps/charmm-gammes/build
$ make -j 16 2>&1 | tee make-charmm.log
$ sudo mkdir -p /share/apps/charmm/c41b2/gcc-5.5.0_mpich2-3.2.1
$ sudo chown -R $USER.apolo /share/apps/charmm/c41b2/gcc-5.5.0_mpich2-3.2.1
$ sudo make install 2>&1 | tee make-charmm.log
$ sudo chown -R root.root /share/apps/charmm/c41b2/gcc-5.5.0_mpich2-3.2.1

5. After finishing with the last parallel make, the charmm binary should have been produced, we can try it as follows:

$ ./charmm
...
1
              Chemistry at HARvard Macromolecular Mechanics
        (CHARMM) - Developmental Version 41b2   February 15, 2017
                             Revision unknown
    Copyright(c) 1984-2014  President and Fellows of Harvard College
                           All Rights Reserved
  Current operating system: Linux-2.6.32-504.16.2.el6.x86_64(x86_64)@deb
              Created on  6/6/17 at  9:36:54 by user: mgomezzul

         aximum number of ATOMS:    360720, and RESidues:      120240
...

Module

#%Module1.0####################################################################
##
## module load charmm/c41b2
##
## /share/apps/modules/charmm/c41b2
## Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp {} {
    global version modroot
    puts stderr "Sets the environment for using CHARMM c41b2\
        \nin the shared directory\
        \n/share/apps/charmm/c41b2\
        \nbuilded with GAMESS 2016 R1, MPICH2 3.2 and GCC-5.4.0"
}

module-whatis "(Name________) charmm"
module-whatis "(Version_____) c41b2"
module-whatis "(Compilers___) mpich2-3.2_gcc-5.4.0"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/charmm/c41b2
set         version       c41b2
set         sys           x86_64-redhat-linux

conflict charmm

module load mpich2/3.2_gcc-5.4.0


prepend-path        PATH            $topdir/bin

Mode of Use

1. Have available an example to run charmm-gamess, in our case the example is available in /home/$USER/test/charm/ilans

cd /home/$USER/test/charmm-gamess/test_ilans

SLURM Template

#!/bin/sh

#!/bin/sh

#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --time=250:00:00
#SBATCH --job-name=mdrun-npt
#SBATCH -o result_%N_%j.out
#SBATCH -e result_%N_%j.err

# Don't share environment variables
export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=1

module load charmm/c41b2_gcc-5.5.0_mpich2-3.2.1

srun --mpi=pmi2 charmm < min1.inp  > pot.out

References

• https://www.charmm.org/charmm/documentation/by-version/c41b1/
• http://ala.cmm.ki.si/gamess/20160818.1/Compile-CHARMM-with-GAMESS.txt
• https://www.charmmtutorial.org/index.php/Installation
• https://github.com/kgullikson88/Telluric-Fitter/issues/5

Author

• Mateo Gómez Zuluaga