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fireball_18.02_ambertools_17 [2018/03/22 19:21] |
fireball_18.02_ambertools_17 [2018/03/22 19:21] jesus |
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+ | ====== Fireball & Amber with EXTERN (mpi) ====== | ||
+ | |||
+ | |||
+ | mkdir fireball | ||
+ | cd fireball | ||
+ | export FIREBALLHOME=$(pwd) | ||
+ | git clone https://github.com/fireball-QMD/progs | ||
+ | cd progs | ||
+ | |||
+ | change in Makefile: | ||
+ | * MACHINE = your options | ||
+ | * PARALLEL = MPI | ||
+ | * METHOD = SCALAPACK | ||
+ | |||
+ | |||
+ | | ||
+ | make server_amber | ||
+ | | ||
+ | |||
+ | Download AmberTools17.tar from http://ambermd.org/ | ||
+ | |||
+ | tar -xvf AmberTools17.tar | ||
+ | cd amber16 | ||
+ | export AMBERHOME=$(pwd) | ||
+ | export MKL_HOME=/opt/intel/composerxe-2011.2.137/mkl/ | ||
+ | cd AmberTools/src | ||
+ | | ||
+ | |||
+ | cp $FIREBALLHOME/progs/QMMM/qm2/qm2_extern_module.F90 $AMBERHOME/AmberTools/src/sander/ | ||
+ | cp $FIREBALLHOME/progs/QMMM/qm2/qm2_extern_fb_module.F90 $AMBERHOME/AmberTools/src/sander/ | ||
+ | cp $FIREBALLHOME/progs/QMMM/qm2/depend $AMBERHOME/AmberTools/src/sander/ | ||
+ | cp $FIREBALLHOME/progs/QMMM/qm2/Makefile.sander.server $AMBERHOME/AmberTools/src/sander/Makefile | ||
+ | cd $AMBERHOME | ||
+ | ./configure -intelmpi intel | ||
+ | make | ||
+ | |||
+ | ====== Run an Example ====== | ||
+ | |||
+ | |||
+ | cd $FIREBALLHOME/progs/QMMM/thym_qmmm | ||
+ | wget http://fireball.ftmc.uam.es/Fdata_HCNO.tar.gz | ||
+ | tar -xvf Fdata_HCNO.tar.gz | ||
+ | mpdboot | ||
+ | mpiexec -n 1 -env I_MPI_DEVICE sock $FIREBALLHOME/progs/fireball_server | ||
+ | mpiexec -n 1 -env I_MPI_DEVICE sock $AMBERHOME/bin/sander.MPI -O -i amber.in -o outmd -p thym_qmmm.prmtop -c thym_qmmm.inpcrd -x answer.mdcrd -r answer.rst | ||
+ | |||
+ | |||