Merge pull request #1575 from davydden/pkg/nwchem

nwchem: add new package
spack · Aug 24, 2016 · 63859bf · 63859bf
2 parents 5cfa748 + d154f15
commit 63859bf
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diff --git a/var/spack/repos/builtin/packages/nwchem/Config_libs66.patch b/var/spack/repos/builtin/packages/nwchem/Config_libs66.patch
@@ -0,0 +1,46 @@
+Index: src/config/makefile.h
+===================================================================
+--- src/config/makefile.h	(revision 27729)
++++ src/config/makefile.h	(revision 27844)
+@@ -2257,11 +2258,7 @@
+   DEFINES += -DFDIST
+ endif
+
+-_TOOLS_BUILD= $(shell [ -e ${NWCHEM_TOP}/src/tools/build/config.h ] && cat ${NWCHEM_TOP}/src/tools/build/config.h | awk ' /HAVE_SQRT/ {print "Y"}')
+-
+-ifeq ($(_TOOLS_BUILD),Y)
+ _USE_SCALAPACK = $(shell cat ${NWCHEM_TOP}/src/tools/build/config.h | awk ' /HAVE_SCALAPACK\ 1/ {print "Y"}')
+-endif
+
+ ifeq ($(_USE_SCALAPACK),Y)
+   DEFINES += -DSCALAPACK
+@@ -2286,8 +2283,8 @@
+ 	      -brename:.pdgetrf_,.pdgetrf \
+ 	      -brename:.pdgetrs_,.pdgetrs 
+ endif
+-  CORE_LIBS += $(ELPA) $(SCALAPACK) $(PBLAS) $(BLACS)
+ endif
++  CORE_LIBS += $(ELPA) $(SCALAPACK)
+
+ ifdef USE_64TO32
+       CORE_LIBS +=  -l64to32
+@@ -2436,18 +2433,11 @@
+  DEFINES += -DUSE_F90_ALLOCATABLE
+ endif
+
+-ifeq ($(_TOOLS_BUILD),Y)
+ # lower level libs used by communication libraries 
+ COMM_LIBS=  $(shell grep ARMCI_NETWORK_LIBS\ = ${NWCHEM_TOP}/src/tools/build/Makefile | cut -b 22-)
+ COMM_LIBS +=  $(shell grep ARMCI_NETWORK_LDFLAGS\ = ${NWCHEM_TOP}/src/tools/build/Makefile | cut -b 24-)
+ #comex bit
+-HAVE_COMEX = $(shell [ -e ${NWCHEM_TOP}/src/tools/build/comex/config.h ] && cat ${NWCHEM_TOP}/src/tools/build/comex/config.h| grep COMEX_NETWORK| awk ' / 1/ {print "Y"}')
+-ifeq ($(HAVE_COMEX),Y)
+-COMM_LIBS +=  $(shell grep LIBS\ = ${NWCHEM_TOP}/src/tools/build/comex/Makefile|grep -v _LIBS| cut -b 8-)
+-#we often need pthread, let's add it
+-COMM_LIBS += -lpthread
+-endif
+-endif
++COMM_LIBS +=  $(shell [ -e ${NWCHEM_TOP}/src/tools/build/comex/config.h ] && grep LIBS\ = ${NWCHEM_TOP}/src/tools/build/comex/Makefile|grep -v _LIBS| cut -b 8-) -lpthread
+ ifdef COMM_LIBS 
+  CORE_LIBS += $(COMM_LIBS) 
+ endif 
diff --git a/var/spack/repos/builtin/packages/nwchem/Gcc6_macs_optfix.patch b/var/spack/repos/builtin/packages/nwchem/Gcc6_macs_optfix.patch
@@ -0,0 +1,40 @@
+Index: src/config/makefile.h
+===================================================================
+--- src/config/makefile.h	(revision 28470)
++++ src/config/makefile.h	(revision 28471)
+@@ -910,6 +910,7 @@
+         GNUMINOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c24)
+         GNU_GE_4_6 = $(shell [ $(GNUMAJOR) -gt 4 -o \( $(GNUMAJOR) -eq 4 -a $(GNUMINOR) -ge 6 \) ] && echo true)
+         GNU_GE_4_8 = $(shell [ $(GNUMAJOR) -gt 4 -o \( $(GNUMAJOR) -eq 4 -a $(GNUMINOR) -ge 8 \) ] && echo true)
++        GNU_GE_6 = $(shell [ $(GNUMAJOR) -ge 6  ] && echo true)
+         endif
+         ifeq ($(GNU_GE_4_6),true)
+         DEFINES  += -DGCC46
+@@ -921,6 +922,9 @@
+
+           FOPTIONS += -Warray-bounds
+         endif
++        ifeq ($(GNU_GE_6),true)
++         FOPTIMIZE += -fno-tree-dominator-opts # solvation/hnd_cosmo_lib breaks
++        endif
+         ifdef USE_OPENMP
+            FOPTIONS  += -fopenmp
+            LDOPTIONS += -fopenmp
+@@ -1067,6 +1071,7 @@
+         GNUMINOR=$(shell $(FC) -dM -E - < /dev/null 2> /dev/null | egrep __VERS | cut -c24)
+         GNU_GE_4_6 = $(shell [ $(GNUMAJOR) -gt 4 -o \( $(GNUMAJOR) -eq 4 -a $(GNUMINOR) -ge 6 \) ] && echo true)
+         GNU_GE_4_8 = $(shell [ $(GNUMAJOR) -gt 4 -o \( $(GNUMAJOR) -eq 4 -a $(GNUMINOR) -ge 8 \) ] && echo true)
++        GNU_GE_6 = $(shell [ $(GNUMAJOR) -ge 6  ] && echo true)
+         ifeq ($(GNU_GE_4_6),true)
+          DEFINES  += -DGCC46
+         endif
+@@ -1076,6 +1081,9 @@
+ #gone          FFLAGS_FORGA += -fno-aggressive-loop-optimizations
+           FOPTIONS += -Warray-bounds
+         endif # GNU_GE_4_8
++        ifeq ($(GNU_GE_6),true)
++         FOPTIMIZE += -fno-tree-dominator-opts # solvation/hnd_cosmo_lib breaks
++        endif
+         endif # GNUMAJOR
+
+         ifdef USE_OPENMP
diff --git a/var/spack/repos/builtin/packages/nwchem/Gcc6_optfix.patch b/var/spack/repos/builtin/packages/nwchem/Gcc6_optfix.patch
@@ -0,0 +1,21 @@
+--- src/config/makefile.h.orig	2016-07-22 08:45:52.100229544 -0700
++++ src/config/makefile.h	2016-07-22 08:49:00.321422169 -0700
+@@ -1565,6 +1565,7 @@
+         GNU_GE_4_6 = $(shell [ $(GNUMAJOR) -gt 4 -o \( $(GNUMAJOR) -eq 4 -a $(GNUMINOR) -ge 6 \) ] && echo true)
+         GNU_GE_4_8 = $(shell [ $(GNUMAJOR) -gt 4 -o \( $(GNUMAJOR) -eq 4 -a $(GNUMINOR) -ge 8 \) ] && echo true)
+         endif
++        GNU_GE_6 = $(shell [ $(GNUMAJOR) -ge 6  ] && echo true)
+         ifeq ($(GNU_GE_4_6),true)
+           DEFINES  += -DGCC46
+         endif
+@@ -1942,6 +1943,10 @@
+         FOPTIMIZE  += -O3 
+         FOPTIMIZE  += -mfpmath=sse -ffast-math
+         FOPTIMIZE  += -fprefetch-loop-arrays #-ftree-loop-linear
++        ifeq ($(GNU_GE_6),true)
++         FOPTIMIZE += -fno-tree-dominator-opts # solvation/hnd_cosmo_lib breaks
++        endif
++
+         ifeq ($(GNU_GE_4_8),true)
+           FOPTIMIZE  += -ftree-vectorize   -fopt-info-vec
+         endif
diff --git a/var/spack/repos/builtin/packages/nwchem/Util_getppn.patch b/var/spack/repos/builtin/packages/nwchem/Util_getppn.patch
@@ -0,0 +1,15 @@
+Index: src/util/util_getppn.c
+===================================================================
+--- src/util/util_getppn.c	(revision 27443)
++++ src/util/util_getppn.c	(working copy)
+@@ -32,7 +33,9 @@
+ void FATR util_getppn_(Integer *ppn_out){
+
+ #if defined(__bgq__)
+-    *ppn_out = Kernel_ProcessCount();
++  *ppn_out = (Integer) Kernel_ProcessCount();
++  return;
++  if(0) {
+ #elif MPI_VERSION >= 3
+
+     int err;
diff --git a/var/spack/repos/builtin/packages/nwchem/Util_gnumakefile.patch b/var/spack/repos/builtin/packages/nwchem/Util_gnumakefile.patch
@@ -0,0 +1,21 @@
+Index: src/util/GNUmakefile
+===================================================================
+--- src/util/GNUmakefile	(revision 27774)
++++ src/util/GNUmakefile	(revision 27782)
+@@ -234,7 +234,7 @@
+
+     USES_BLAS = util.fh ga_it_lsolve.F ga_maxelt.F ga_mix.F ga_iter_diag.F \
+                 ga_orthog.F dabsmax.F ga_normf.F corr_mk_ref.F ga_it2.F ga_lkain_ext.F util_file_name.F dgefa.f util_patch_test.F stpr_sjacobi.F util_dgeev.F \
+-		util_test_cholesky.F
++		util_test_cholesky.F dfill.f ga_lkain_2cpl3_ext.F ga_it2.F
+
+ ifdef SPEECH
+    LIB_DEFINES += -DSPEECH
+@@ -254,6 +254,7 @@
+ ifeq ($(TARGET),$(findstring $(TARGET),BGL BGP BGQ))
+ DEFINES += -DNEED_LOC
+ LIB_DEFINES += -DNO_UTIL_TESTS
++LIB_DEFINES += -I/bgsys/drivers/ppcfloor/firmware/include -I/bgsys/drivers/ppcfloor/spi/include/kernel
+ endif
+
+ ifdef SLURM
diff --git a/var/spack/repos/builtin/packages/nwchem/cosmo_dftprint.patch b/var/spack/repos/builtin/packages/nwchem/cosmo_dftprint.patch
@@ -0,0 +1,26 @@
+Index: src/nwdft/scf_dft/dft_scf.F
+===================================================================
+--- src/nwdft/scf_dft/dft_scf.F	(revision 28116)
++++ src/nwdft/scf_dft/dft_scf.F	(revision 28117)
+@@ -1884,6 +1884,13 @@
+          if (abs(Edisp).gt.0.0d0) then
+           write(LuOut,224)Edisp
+          endif
++         if (cosmo_on.and.cosmo_phase.eq.2) then
++          if (do_cosmo_smd) then
++           write(LuOut,225) ecosmo+gcds
++          else
++           write(LuOut,225) ecosmo
++          end if
++         endif
+          if (do_zora) write(luout,2221) ener_scal
+          write(luout,2222) rho_n
+          write(luout,2223) dft_time
+@@ -2457,6 +2464,7 @@
+      &     '       Correlation energy =', f22.12/
+      &     ' Nuclear repulsion energy =', f22.12/)
+  224  format('    Dispersion correction =', f22.12/)
++ 225  format('             COSMO energy =', f22.12/)
+ c
+  2221 format('       Scaling correction =', f22.12/)
+  2222 format(' Numeric. integr. density =', f22.12/)
diff --git a/var/spack/repos/builtin/packages/nwchem/cosmo_meminit.patch b/var/spack/repos/builtin/packages/nwchem/cosmo_meminit.patch
@@ -0,0 +1,172 @@
+Index: src/solvation/hnd_cosmo_lib.F
+===================================================================
+--- src/solvation/hnd_cosmo_lib.F	(revision 27880)
++++ src/solvation/hnd_cosmo_lib.F	(revision 27881)
+@@ -92,26 +92,32 @@
+ c    &    i_init,init))
+ c    & call errquit('hnd_cosset, malloc of init  failed',911,MA_ERR)
+ c
+-      stat = .true.
+-      stat = stat.and.ma_push_get(mt_dbl,3*nat,"xyzatm",l_i10,i10)
+-      stat = stat.and.ma_push_get(mt_dbl,  nat,"ratm",l_i20,i20)
+-      stat = stat.and.ma_push_get(mt_int,  nat,"nspa",l_i30,i30)
+-      stat = stat.and.ma_push_get(mt_int,  nat,"nppa",l_i40,i40)
+-      stat = stat.and.ma_push_get(mt_int,3*mxface,"ijkfac",l_i50,i50)
+-      stat = stat.and.ma_push_get(mt_dbl,3*mxface,"xyzseg",l_i60,i60)
+-      stat = stat.and.ma_push_get(mt_int,  mxface,"ijkseg",l_i70,i70)
+-      stat = stat.and.ma_push_get(mt_log,  mxface*nat,"insseg",
+-     &                                                l_i80,i80)
+-      stat = stat.and.ma_push_get(mt_dbl,3*mxface*nat,"xyzspa",
+-     &                                                l_i90,i90)
+-      stat = stat.and.ma_push_get(mt_int,  mxface*nat,"ijkspa",
+-     &                                                l_i100,i100)
+-      stat = stat.and.ma_push_get(mt_int,  mxface*nat,"numpps",
+-     &                                                l_i110,i110)
+-      stat = stat.and.ma_push_get(mt_dbl,3*mxapex    ,"apex",
+-     &                                                l_i120,i120)
+-      stat = stat.and.ma_push_get(mt_dbl,  mxface*nat,"xyzff",
+-     &                                                l_i130,i130)
++      if(.not.ma_push_get(mt_dbl,3*nat,"xyzatm",l_i10,i10))
++     c     call errquit('hndcosset: not enuf mem',0,MA_ERR)
++      if(.not.ma_push_get(mt_dbl,  nat,"ratm",l_i20,i20))
++     c     call errquit('hndcosset: not enuf mem',1,MA_ERR)
++      if(.not.ma_push_get(mt_int,  nat,"nspa",l_i30,i30))
++     c     call errquit('hndcosset: not enuf mem',2,MA_ERR)
++      if(.not.ma_push_get(mt_int,  nat,"nppa",l_i40,i40))
++     c     call errquit('hndcosset: not enuf mem',3,MA_ERR)
++      if(.not.ma_push_get(mt_int,3*mxface,"ijkfac",l_i50,i50))
++     c     call errquit('hndcosset: not enuf mem',4,MA_ERR)
++      if(.not.ma_push_get(mt_dbl,3*mxface,"xyzseg",l_i60,i60))
++     c     call errquit('hndcosset: not enuf mem',5,MA_ERR)
++      if(.not.ma_push_get(mt_int,  mxface,"ijkseg",l_i70,i70))
++     c     call errquit('hndcosset: not enuf mem',6,MA_ERR)
++      if(.not.ma_push_get(mt_log,  mxface*nat,"insseg",l_i80,i80))
++     c     call errquit('hndcosset: not enuf mem',7,MA_ERR)
++      if(.not.ma_push_get(mt_dbl,3*mxface*nat,"xyzspa",l_i90,i90))
++     c     call errquit('hndcosset: not enuf mem',8,MA_ERR)
++      if(.not.ma_push_get(mt_int,  mxface*nat,"ijkspa",l_i100,i100))
++     c     call errquit('hndcosset: not enuf mem',9,MA_ERR)
++      if(.not.ma_push_get(mt_int,  mxface*nat,"numpps",l_i110,i110))
++     c     call errquit('hndcosset: not enuf mem',10,MA_ERR)
++      if(.not.ma_push_get(mt_dbl,3*mxapex    ,"apex",l_i120,i120))
++     c     call errquit('hndcosset: not enuf mem',11,MA_ERR)
++      if(.not.ma_push_get(mt_dbl,  mxface*nat,"xyzff",l_i130,i130))
++     c     call errquit('hndcosset: not enuf mem',12,MA_ERR)
+ c     i10 =init                    ! xyzatm(3,nat)
+ c     i20 =i10 +3*nat              !   ratm(  nat)
+ c     i30 =i20 +  nat              !   nspa(  nat)
+@@ -129,9 +135,10 @@
+ c
+       call hnd_cossrf(nat,c,radius,nat,mxface,mxapex,
+      1                dbl_mb(i10),dbl_mb(i20),int_mb(i30),int_mb(i40),
+-     2                int_mb(i50),dbl_mb(i60),int_mb(i70),
+-     3                log_mb(i80),dbl_mb(i90),int_mb(i100),int_mb(i110),
++     2                int_mb(i50),dbl_mb(i60),int_mb(i70),log_mb(i80),
++     3                dbl_mb(i90),int_mb(i100),int_mb(i110),
+      4                dbl_mb(i120),dbl_mb(i130),rtdb)
++
+ c
+ c     ----- release memory block -----
+ c
+@@ -157,7 +164,7 @@
+ #include "global.fh"
+ #include "stdio.fh"
+ #include "cosmoP.fh"
+-c
++#include "mafdecls.fh"
+       integer rtdb, nat
+       integer mxatm
+       integer mxfac
+@@ -261,6 +268,7 @@
+ c
+ c     ----- create -solvent accessible surface- of the molecule -----
+ c
++
+       call hnd_cossas(nat,xyzatm,ratm,mxatm,
+      1                nspa,nppa,xyzspa,ijkspa,
+      2                nseg,nfac,xyzseg,ijkseg,insseg,
+@@ -366,6 +374,7 @@
+ #include "stdio.fh"
+ #include "bq.fh"
+ #include "prop.fh"
++cnew
+ #include "cosmoP.fh"
+ c
+       integer rtdb    !< [Input] The RTDB handle
+@@ -410,7 +419,6 @@
+       integer          numpps(  mxface,mxatom)
+       double precision  xyzff(  mxface,mxatom)
+       double precision zero, one
+-      data zero    /0.0d+00/
+       data one     /1.0d+00/
+       integer l_efcc, k_efcc, l_efcs, k_efcs, l_efcz, k_efcz
+       integer l_efclb, k_efclb, k_efciat, l_efciat
+@@ -464,7 +472,7 @@
+          do i=1,mxface
+             ijkspa(i,iat)=0
+             numpps(i,iat)=0
+-            xyzff(i,iat)=zero
++            xyzff(i,iat)=0d0
+          enddo
+       enddo
+ c
+@@ -473,7 +481,7 @@
+ c
+       do iat=1,nat
+ c
+-         if(ratm(iat).ne.zero) then
++         if(ratm(iat).ne.0d0) then
+             do iseg=1,nseg
+                ijkspa(iseg,iat)=ijkseg(iseg)
+                xyzff(iseg,iat)=one
+@@ -515,7 +523,7 @@
+                    enddo
+                  endif
+                else if (do_cosmo_model.eq.DO_COSMO_YK) then
+-                 if((jat.ne.iat).and.(ratm(jat).ne.zero)
++                 if((jat.ne.iat).and.(ratm(jat).ne.0d0)
+      1                        .and.(dij.lt.(ratm(iat)+rout(jat)))) then
+                    do iseg=1,nseg
+                      dum=dist(xyzspa(1,iseg,iat),
+@@ -615,7 +623,7 @@
+ c
+       nefc = 0
+       do iat=1,nat
+-         if(ratm(iat).ne.zero) then
++         if(ratm(iat).ne.0d0) then
+             do iseg=1,nseg
+                if(.not.insseg(iseg,iat)) nefc = nefc+1
+             enddo
+@@ -639,11 +647,11 @@
+ c           save segment surfaces
+ c           save segment to atom mapping
+ c
+-      srfmol=zero
+-      volmol=zero
++      srfmol=0d0
++      volmol=0d0
+       ief   =0
+       do iat=1,nat
+-         if(ratm(iat).ne.zero) then
++         if(ratm(iat).ne.0d0) then
+             if (do_cosmo_model.eq.DO_COSMO_KS) then
+               ratm_real=ratm(iat)-rsolv/bohr
+             else if (do_cosmo_model.eq.DO_COSMO_YK) then
+@@ -720,7 +728,7 @@
+       endif
+ c
+       do ief=1,nefc
+-         dbl_mb(k_efcz+ief-1)=zero
++         dbl_mb(k_efcz+ief-1)=0d0
+       enddo
+       do ief=1,nefc
+          byte_mb(k_efclb+(ief-1)*8)='        '
+@@ -877,6 +885,8 @@
+       implicit double precision (a-h,o-z)
+ #include "global.fh"
+ #include "stdio.fh"
++cnew
++#include "cosmoP.fh"
+ c
+ c              ----- starting from -icosahedron- -----
+ c
diff --git a/var/spack/repos/builtin/packages/nwchem/dplot_tolrho.patch b/var/spack/repos/builtin/packages/nwchem/dplot_tolrho.patch
@@ -0,0 +1,45 @@
+Index: src/dplot/dplot_input.F
+===================================================================
+--- src/dplot/dplot_input.F	(revision 27986)
++++ src/dplot/dplot_input.F	(revision 27987)
+@@ -63,6 +63,7 @@
+       iroot     = 1
+       ltransden = .true.
+       ldiffden = .false.
++      tol_rho = 1d-40
+ c
+ c     try to get a scf movecs
+ c
+@@ -263,10 +264,10 @@
+       goto 10
+ c
+  1998 continue
+-      tol_rho = 1d-15
+       If (.not. inp_f(tol_rho))
+      &  Call ErrQuit('DPlot_Input: failed to read tol_rho',0,
+      &     INPUT_ERR)
++      tol_rho=max(1d-99,tol_rho)
+       goto 10
+ c
+  1999 continue
+Index: src/dplot/dplot_dump.F
+===================================================================
+--- src/dplot/dplot_dump.F	(revision 27986)
++++ src/dplot/dplot_dump.F	(revision 27987)
+@@ -90,7 +90,7 @@
+      .              No_Of_Spacings(3))
+ 99498          format(6E13.5)
+             enddo
+-            else
++         else
+             Do i = 1, nGrid
+                Write(Out_Unit,'(f15.10)')values(i)
+             End Do
+@@ -107,6 +107,7 @@
+             End Do
+             AppCh = Sum*Volume
+             Write(LuOut,*)
++            Write(LuOut,'(a,e30.5)')'  Tol_rho              = ',tol_rho
+             Write(LuOut,'(a,f30.5)')'  Sum of elements      = ',sum
+             Write(LuOut,'(a,f30.5)')'  Integration volume   = ',volume
+             Write(LuOut,'(a,f30.5)')'  Integrated Charge    = ',AppCh