Update 21 May 2013: The execution times can be improved considerably by setting
ARMCI_NETWORK=SOCKETS
They are still ca 30% longer than 6.1.1 though due to slower SCF convergence. See http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id834/Nwchem_6.3_running_2-5_times_slo....html
Update 20 May 2013: I did a bit of basic benchmarking. NWChem 6.3 is incredibly slow (ca 190s vs 40s for the 8 core, 3.6 GHz benchmark in http://verahill.blogspot.com.au/2013/05/414-frequency-vs-cores-crude.html). It's parallellising properly from what I can see (i.e. it is not running 8 serial jobs). I've repeated the calc with an unpatched version of nwchem 6.3, and it is just as slow.
I'll post updates here if I figure this one out.
Original post:
NWChem 6.3 is just out. Here's how to build it for CPU computations.
To build on CentOS 5.6, see http://verahill.blogspot.com.au/2013/05/421-nwchem-63-on-rocks-543centos-56.html
Math library:
Use either openblas (for intel or AMD) or ACML (for AMD).
- To set up Openblas, see here: http://verahill.blogspot.com.au/2013/05/423-openblas-on-debian-wheezy.html
- To set up ACML, see here: http://verahill.blogspot.com.au/2013/05/422-set-up-acml-on-linux.html
My GabEdit/Python NWChem patch
This is NOT the patch alluded to in the 23 May update and is optional. It enables python support, and makes the output more verbose so that gabedit can be used as an alternative to ECCE. Hence, it is required if, but only if, you want to enable python and to be able to use GabEdit to open output files.
First create a patch file, e.g. diff.patch.
diff -rupN src.original/config/makefile.h src/config/makefile.h
--- src.original/config/makefile.h 2013-04-15 12:41:45.016853322 +1000
+++ src/config/makefile.h 2013-04-15 12:38:44.933319544 +1000
@@ -2039,7 +2039,7 @@ endif
ifeq ($(BUILDING_PYTHON),python)
# EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl
- EXTRA_LIBS += -lnwcutil -lpthread -lutil -ldl
+ EXTRA_LIBS += -lnwcutil -lpthread -lutil -ldl -lssl -lz
LDOPTIONS = -Wl,--export-dynamic
endif
ifeq ($(NWCHEM_TARGET),CATAMOUNT)
diff -rupN src.original/ddscf/movecs_pr_anal.F src/ddscf/movecs_pr_anal.F
--- src.original/ddscf/movecs_pr_anal.F 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/movecs_pr_anal.F 2013-04-15 12:23:28.100409225 +1000
@@ -195,7 +195,7 @@ c
22 format(1x,2(' Bfn. Coefficient Atom+Function ',5x))
write(LuOut,23)
23 format(1x,2(' ----- ------------ ---------------',5x))
- do klo = 0, min(n-1,9), 2
+ do klo = 0, min(n-1,199), 2
khi = min(klo+1,n-1)
write(LuOut,2) (
$ int_mb(k_list+k)+1,
diff -rupN src.original/ddscf/rohf.F src/ddscf/rohf.F
--- src.original/ddscf/rohf.F 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/rohf.F 2013-04-15 12:23:28.100409225 +1000
@@ -153,7 +153,7 @@ c
ilo = 1
ihi = nmo
endif
- call movecs_print_anal(basis, ilo, ihi, 0.15d0, g_movecs,
+ call movecs_print_anal(basis, ilo, ihi, 0.01d0, g_movecs,
$ 'ROHF Final Molecular Orbital Analysis',
$ .true., dbl_mb(k_eval), oadapt, int_mb(k_irs),
$ .true., dbl_mb(k_occ))
diff -rupN src.original/ddscf/scf_vec_guess.F src/ddscf/scf_vec_guess.F
--- src.original/ddscf/scf_vec_guess.F 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/scf_vec_guess.F 2013-04-15 12:23:28.100409225 +1000
@@ -511,19 +511,19 @@ c
nprint = min(nclosed+nopen+30,nmo)
if (scftype.eq.'RHF' .or. scftype.eq.'ROHF') then
call movecs_print_anal(basis, 1,
- & nprint, 0.15d0, g_movecs,
+ & nprint, 0.01d0, g_movecs,
& 'ROHF Initial Molecular Orbital Analysis',
& .true., dbl_mb(k_eval), oadapt, int_mb(k_irs),
& .true., dbl_mb(k_occ))
else
nprint = min(nalpha+20,nmo)
call movecs_print_anal(basis, max(1,nbeta-20),
- & nprint, 0.15d0, g_movecs,
+ & nprint, 0.01d0, g_movecs,
& 'UHF Initial Alpha Molecular Orbital Analysis',
& .true., dbl_mb(k_eval), oadapt, int_mb(k_irs),
& .true., dbl_mb(k_occ))
call movecs_print_anal(basis, max(1,nbeta-20),
- & nprint, 0.15d0, g_movecs(2),
+ & nprint, 0.01d0, g_movecs(2),
& 'UHF Initial Beta Molecular Orbital Analysis',
& .true., dbl_mb(k_eval+nbf), oadapt, int_mb(k_irs+nmo),
& .true., dbl_mb(k_occ+nbf))
diff -rupN src.original/ddscf/uhf.F src/ddscf/uhf.F
--- src.original/ddscf/uhf.F 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/uhf.F 2013-04-15 12:23:28.096409414 +1000
@@ -144,11 +144,11 @@ C
enddo
ihi = max(ihi-1,1)
9611 continue
- call movecs_print_anal(basis, ilo, ihi, 0.15d0, g_movecs,
+ call movecs_print_anal(basis, ilo, ihi, 0.01d0, g_movecs,
$ 'UHF Final Alpha Molecular Orbital Analysis',
$ .true., dbl_mb(k_eval), oadapt, int_mb(k_irs),
$ .true., dbl_mb(k_occ))
- call movecs_print_anal(basis, ilo, ihi, 0.15d0, g_movecs(2),
+ call movecs_print_anal(basis, ilo, ihi, 0.01d0, g_movecs(2),
$ 'UHF Final Beta Molecular Orbital Analysis',
$ .true., dbl_mb(k_eval+nbf), oadapt, int_mb(k_irs+nmo),
$ .true., dbl_mb(k_occ+nbf))
diff -rupN src.original/mcscf/mcscf.F src/mcscf/mcscf.F
--- src.original/mcscf/mcscf.F 2013-04-15 12:41:45.000854073 +1000
+++ src/mcscf/mcscf.F 2013-04-15 12:23:23.748613695 +1000
@@ -719,7 +719,7 @@ c
if (util_print('final vectors analysis', print_default))
$ call movecs_print_anal(basis,
$ max(1,nclosed-10), min(nbf,nclosed+nact+10),
- $ 0.15d0, g_movecs, 'Analysis of MCSCF natural orbitals',
+ $ 0.01d0, g_movecs, 'Analysis of MCSCF natural orbitals',
$ .true., dbl_mb(k_evals), .true., int_mb(k_sym),
$ .true., dbl_mb(k_occ))
c
diff -rupN src.original/nwdft/scf_dft/dft_mxspin_ovlp.F src/nwdft/scf_dft/dft_mxspin_ovlp.F
--- src.original/nwdft/scf_dft/dft_mxspin_ovlp.F 2013-04-15 12:41:45.604825677 +1000
+++ src/nwdft/scf_dft/dft_mxspin_ovlp.F 2013-04-15 12:23:28.228403211 +1000
@@ -184,14 +184,14 @@ c
call ga_sync()
c
call movecs_print_anal(basis,int_mb(k_non),int_mb(k_non)
- & ,0.15d0,g_alpha,'Alpha Orbitals without Beta Partners',
+ & ,0.01d0,g_alpha,'Alpha Orbitals without Beta Partners',
& .false., 0.0 ,.false., 0 , .false., 0 )
c
if (nct.GE.2) then
do i = 2,nct
ind = int_mb(k_non+i-1)
call movecs_print_anal(basis,ind,ind
- & ,0.15d0,g_alpha,' ',
+ & ,0.01d0,g_alpha,' ',
& .false., 0.0 ,.false., 0 , .false., 0 )
enddo
endif
@@ -350,7 +350,7 @@ c endif
c endif
c 9990 format(/,18x,'THERE ARE',i3,1x,'UN-PARTNERED ALPHA ORBITALS')
c
- call movecs_print_anal(basis, 1, nalp, 0.15d0, g_ualpha,
+ call movecs_print_anal(basis, 1, nalp, 0.01d0, g_ualpha,
& 'Alpha Orb. w/o Beta Partners (after maxim. alpha/beta overlap)',
& .false., 0.0 ,.false., 0 , .false., 0 )
c
diff -rupN src.original/nwdft/scf_dft/dft_scf.F src/nwdft/scf_dft/dft_scf.F
--- src.original/nwdft/scf_dft/dft_scf.F 2013-04-15 12:41:45.608825490 +1000
+++ src/nwdft/scf_dft/dft_scf.F 2013-04-15 12:23:28.228403211 +1000
@@ -1774,7 +1774,7 @@ c
else
blob='DFT Final Beta Molecular Orbital Analysis'
endif
- call movecs_print_anal(ao_bas_han, ilo, ihi, 0.15d0,
+ call movecs_print_anal(ao_bas_han, ilo, ihi, 0.01d0,
& g_movecs(ispin),
& blob,
& .true., dbl_mb(k_eval(ispin)), oadapt,
diff -rupN src.original/nwdft/scf_dft_cg/dft_cg_solve.F src/nwdft/scf_dft_cg/dft_cg_solve.F
--- src.original/nwdft/scf_dft_cg/dft_cg_solve.F 2013-04-15 12:41:45.612825303 +1000
+++ src/nwdft/scf_dft_cg/dft_cg_solve.F 2013-04-15 12:23:28.220403588 +1000
@@ -183,7 +183,7 @@ c
blob = 'DFT Final Beta Molecular Orbital Analysis'
endif
call movecs_fix_phase(g_movecs(ispin))
- call movecs_print_anal(basis, ilo, ihi, 0.15d0,
+ call movecs_print_anal(basis, ilo, ihi, 0.01d0,
& g_movecs(ispin),blob,
& .true., dbl_mb(k_eval+(ispin-1)*nbf),
& oadapt, int_mb(k_irs+(ispin-1)*nbf),
Compile NWChem
This examples uses the ACML libs. See e.g. this post for openblas settings.
sudo apt-get install build-essential gfortran python2.7-dev libopenmpi-dev openmpi-bin sudo mkdir /opt/nwchem sudo chown $USER:$USER /opt/nwchem cd /opt/nwchem/ wget http://www.nwchem-sw.org/download.php?f=Nwchem-6.3-src.2013-05-17.tar.gz mv download.php\?f\=Nwchem-6.3-src.2013-05-17.tar.gz Nwchem-6.3-src.2013-05-17.tar.gz tar xvf Nwchem-6.3-src.2013-05-17.tar.gz cd nwchem-6.3-src.2013-05-17/ patch -p0 < diff.patchpatching file src/config/makefile.h patching file src/ddscf/movecs_pr_anal.F patching file src/ddscf/rohf.F patching file src/ddscf/scf_vec_guess.F patching file src/ddscf/uhf.F patching file src/mcscf/mcscf.F patching file src/nwdft/scf_dft/dft_mxspin_ovlp.F patching file src/nwdft/scf_dft/dft_scf.F patching file src/nwdft/scf_dft_cg/dft_cg_solve.Fcd src/ wget http://www.nwchem-sw.org/images/Iswtch.patch.gz gzip -d Iswtch.patch patch -p0 < Iswtch.patch cd ../ export LARGE_FILES=TRUE export TCGRSH=/usr/bin/ssh export NWCHEM_TOP=`pwd` export NWCHEM_TARGET=LINUX64 export NWCHEM_MODULES="all python" export PYTHONVERSION=2.7 export PYTHONHOME=/usr export BLASOPT="-L/opt/acml/acml5.3.1/gfortran64_int64/lib -lacml" export USE_MPI=y export USE_MPIF=y export USE_MPIF4=y export MPI_LOC=/usr/lib/openmpi/lib export MPI_INCLUDE=/usr/lib/openmpi/include export LIBRARY_PATH="$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/acml/acml5.3.1/gfortran64_int64/lib" export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread" export ARMCI_NETWORK=SOCKETS cd $NWCHEM_TOP/src make clean make nwchem_config make FC=gfortran 1> make.log 2>make.err cd $NWCHEM_TOP/contrib export FC=gfortran ./getmem.nwchem
Settings
Create /opt/nwchem/default.nwchemrc
nwchem_basis_library /opt/nwchem/nwchem-6.3-src.2013-05-17/src/basis/libraries/ ffield amber amber_1 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_s/ amber_2 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_x/ amber_3 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_q/ amber_4 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_u/ amber_5 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/custom/ spce /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/solvents/spce.rst charmm_s /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/charmm_s/ charmm_x /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/charmm_x/
Symmlink to this file in each user's home:
ln -s /opt/nwchem/default.nwchemrc ~/.nwchemrc
No comments:
Post a Comment