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DOMDEC compilation error
#37574 07/24/19 03:17 PM
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I tried to recompile CHARMM with DOMDEC using:

./install.com gnu xxlarge M APH +PARALGROUPS
./installl.com gnu xxlarge M +DOMDEC +PARALGROUPS
./installl.com gnu xxlarge M mpif90 +DOMDEC +PARALGROUPS

But I obtain the following error:

mpif90 -DGNU -DKEY_GNU=1 -DKEY_UNIX=1 -DKEY_MPI=1 -DKEY_PARALLEL=1 -DKEY_PARAFULL=1 -DKEY_EXPAND=1 -DKEY_PUTFCM=1 -DKEY_ACE=1 -DKEY_ADUMB=1 -DKEY_AFM=1 -DKEY_ASPENER=1 -DKEY_ASPMEMB=1 -DKEY_AXD=1 -DKEY_BLOCK=1 -DKEY_CFF=1 -DKEY_CGENFF=1 -DKEY_CHEQ=1 -DKEY_CMAP=1 -DKEY_CONSHELIX=1 -DKEY_CPATH=1 -DKEY_DIMB=1 -DKEY_DMCONS=1 -DKEY_DOCK=1 -DKEY_DYNVV2=1 -DKEY_EMAP=1 -DKEY_EPMF=1 -DKEY_ESTATS=1 -DKEY_FASTEW=1 -DKEY_FLEXPARM=1 -DKEY_FLUCQ=1 -DKEY_FMA=1 -DKEY_FOURD=1 -DKEY_FSSHK=1 -DKEY_GBFIXAT=1 -DKEY_GBINLINE=1 -DKEY_HFB=1 -DKEY_HQBM=1 -DKEY_GCMC=1 -DKEY_GENETIC=1 -DKEY_GRID=1 -DKEY_GSBP=1 -DKEY_SMBP=1 -DKEY_HMCOM=1 -DKEY_IMCUBES=1 -DKEY_LARMORD=1 -DKEY_LONEPAIR=1 -DKEY_LRVDW=1 -DKEY_MC=1 -DKEY_MEHMC=1 -DKEY_MMFF=1 -DKEY_MMPT=1 -DKEY_MOLVIB=1 -DKEY_MTPL=1 -DKEY_MULTCAN=1 -DKEY_NBIPS=1 -DKEY_OLDDYN=1 -DKEY_OPLS=1 -DKEY_OVERLAP=1 -DKEY_PATHINT=1 -DKEY_PBEQ=1 -DKEY_PBOUND=1 -DKEY_PERT=1 -DKEY_PHMD=1 -DKEY_PM1=1 -DKEY_PMEPLSMA=1 -DKEY_PNOE=1 -DKEY_PRIMO=1 -DKEY_PRIMSH=1 -DKEY_RDC=1 -DKEY_RDFSOL=1 -DKEY_REPLICA=1 -DKEY_RGYCONS=1 -DKEY_RPATH=1 -DKEY_RXNCOR=1 -DKEY_SASAE=1 -DKEY_SCPISM=1 -DKEY_SGLD=1 -DKEY_SHAPES=1 -DKEY_SHELL=1 -DKEY_SOFTVDW=1 -DKEY_SSNMR=1 -DKEY_TNPACK=1 -DKEY_TPS=1 -DKEY_TRAVEL=1 -DKEY_TSM=1 -DKEY_TSALLIS=1 -DKEY_FITCHG=1 -DKEY_WCA=1 -DKEY_CHEMPERT=1 -DKEY_PROTO=1 -DKEY_SMD=1 -DKEY_COMP2=1 -DKEY_FACTS=1 -DKEY_LOOKUP=1 -DKEY_RMD=1 -DKEY_VALBOND=1 -DKEY_RXNCONS=1 -DKEY_GNN=1 -DKEY_MRMD=1 -DKEY_QCHEM=1 -DKEY_HDGBVDW=1 -DKEY_DENBIAS=1 -DKEY_DHDGB=1 -DKEY_QUANTUM=1 -DKEY_NOGRAPHICS=1 -DKEY_DOMDEC=1 -DKEY_PARALGROUPS=1 -fno-use-linker-plugin -I. -c -O3 -ffree-form -ffixed-line-length-none -ffree-line-length-none -fmax-identifier-length=63 domdec_bonded.F90
/home/pmj/c42b2/source/domdec/domdec_bonded.src:1299:0:

#include "domdec_bonded_kernel.inc"

Fatal Error: domdec_bonded_kernel.inc: No such file or directory
compilation terminated.
domdec.mk:56: recipe for target 'domdec_bonded.o' failed
make: *** [domdec_bonded.o] Error 1

I tried to include the directory with -B/home/pmj/c42b2/source/domdec and -Bhome/pmj/c42b2/source/domdec, but was not really successful.

I would appreciate anyone's help.

Thank you

Re: DOMDEC compilation error
pmj #37575 07/24/19 03:35 PM
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rmv Online Content
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Only the non-free version includes support for DOMDEC, so you may be working with the free version.


Rick Venable
computational chemist

Re: DOMDEC compilation error
rmv #37576 07/24/19 03:38 PM
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pmj Offline OP
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Dear prof. Venable,

I am using c42b2 version of CHARMM (it is written "Developmental Version 42b2" on the header when you try to run it).

Also, in the /source/domdec/ directory there is indeed the missing file "domdec_bonded_kernel.inc" which for some reason is not being found.

Last edited by pmj; 07/24/19 03:49 PM.
Re: DOMDEC compilation error
pmj #37577 07/24/19 04:19 PM
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Following the guidelines in domdec.doc, I just did the following, and it compiled w/o problems:

module load gcc/6.3.0
module load mvapich2/2.3
module load fftw/3.3.7
./install.com gnu M fftw domdec
:
:
install.com> CHARMM Installation is completed.
The CHARMM executable is /u/rvenable/Charmm/c42b2/exec/gnu_M/charmm.

install.com> Phase 3 completed.
Wed Jul 24 12:11:24 EDT 2019


Rick Venable
computational chemist

Re: DOMDEC compilation error
rmv #37581 07/25/19 08:14 AM
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Thanks. I managed to compile it.

Re: DOMDEC compilation error
pmj #37583 07/25/19 02:43 PM
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Dear prof. Venable,

regarding the domdec version of charmm, I see in the documentation it is only possible to use explicit solvent.

Would it be possible to use emap constraints with it? I see emap cons is not on the list of the 42b1 version and was wondering if it has been added in the 42b2 version.

Thank you

Re: DOMDEC compilation error
pmj #37584 07/25/19 03:24 PM
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DOMDEC was specifically designed for solvated systems, and has custom code to accelerate computing water:water interactions.

No idea about EMAP, you may have to try it with DOMDEC and see what happens.


Rick Venable
computational chemist


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