Compilation on Mac OS X

Just Got Here

9:11:33 AM PST - Mon, Jan 16th 2017
Hi, I'm trying to complile nwchem on a Mac running OS X Sierra (10.12.2).I'm following method 2 (using homebrew) from the wiki. Running make results in the following error: configure: error: in `/Users/dvr/Documents/nwchem-6.6/src/tools/build': configure: error: C++ preprocessor "/lib/cpp" fails sanity check See `config.log' for more details make[1]: * [build/config.status] Error 1 make: * [libraries] Error 1 Logfile contents can be found here [1]. Could anyone show me how to fix this? Thanks in advance, Dries

Forum Vet

6:12:15 PM PST - Mon, Jan 16th 2017
Conflicts coming from MacPorts
After looking at your config.log, I can see that 1) you have /opt/local/bin and /opt/local/sbin in your path and 2) that some stuff is picked up from the MacPorts /opt/local location (c++ (MacPorts gcc48 4.8.5_0) 4.8.5) Please don't try to use Homebrew together with MacPorts. Therefore, my suggestion is to - open a shell with a PATH that does not contain the /opt/local/bin MacPorts location - unset the following env. variables (if they are set at all) MPI_LIB MPI_INCLUDE LIBMPI CPP CXX CC

Just Got Here

2:49:27 AM PST - Tue, Jan 17th 2017
Hi Edoapra, Thanks, that fixed the compilation error. Unfortunately, I get a segfault when I try to run a sample SCF geometry optimization of the nitrogen molecule: Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x1177566a9 #1 0x117755a75 #2 0x7fffcb182bb9 Segmentation fault: 11 I pasted the config.log [1], comex/config.log [2] and armci/config.log[3]. Please let me know if you need any further information. Thanks for your time, Dries

Forum Vet

11:47:54 AM PST - Tue, Jan 17th 2017
Quote:Driesvr Jan 17th 1:49 am Hi Edoapra, Thanks, that fixed the compilation error. Unfortunately, I get a segfault when I try to run a sample SCF geometry optimization of the nitrogen molecule: Thanks for your time, Dries Have you installed any of the patches listed at http://nwchemgit.github.io/index.php/Download#Patches_for_the_27746_revision_of_NWChem_6.6 ? Your segfault failure could be fixed by the patch below http://nwchemgit.github.io/download.php?f=Ga_argv.patch.gz Here is how to apply it cd $NWCHEM_TOP wget http://nwchemgit.github.io/images/Ga_argv.patch.gz gzip -d Ga_argv.patch.gz patch -p0 < Ga_argv.patch cd tools make cd .. make link

Just Got Here

6:04:59 PM PDT - Sun, Jul 23rd 2017
I've applied the Ga_argv patch and am still getting a similar segfault. I've also applied the Ga_defs, Gcc6_macs, and Gcc6_optfix patches. I'm compiling with open-mpi from homebrew on sierra 10.12.6 following the directions on the compilation page. The GCC version is presently 7.1.0. config.log from the tools directory can be found here [1]. Thanks in advance for your help. Matt Reuter

Forum Vet

12:34:58 PM PDT - Mon, Jul 24th 2017
Matt I could not spot any obvious problem in your config.log Could you please send the output of the command "make link"?

Just Got Here

4:02:19 AM PDT - Tue, Jul 25th 2017

Hi Edo,
Here it is.

/Library/Developer/CommandLineTools/usr/bin/make nwchem.o stubs.o
gfortran -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I.  -I/Users/mgreuter/Documents/Research/Codes/nwchem/6.6/src/include -I/Users/mgreuter/Documents/Research/Codes/nwchem/6.6/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/Users/mgreuter/Documents/Research/Codes/nwchem/6.6'" -DNWCHEM_BRANCH="'6.6'"  -c -o nwchem.o nwchem.F
gfortran -cpp  -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations  -I.  -I/Users/mgreuter/Documents/Research/Codes/nwchem/6.6/src/include -I/Users/mgreuter/Documents/Research/Codes/nwchem/6.6/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/Users/mgreuter/Documents/Research/Codes/nwchem/6.6'" -DNWCHEM_BRANCH="'6.6'"  -c -o stubs.o stubs.F
gfortran  -L/Users/mgreuter/Documents/Research/Codes/nwchem/6.6/lib/MACX64 -L/Users/mgreuter/Documents/Research/Codes/nwchem/6.6/src/tools/install/lib  -o /Users/mgreuter/Documents/Research/Codes/nwchem/6.6/bin/MACX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -ldplot -lvscf -letrans -ltce -lbq -lcons -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -lnwclapack  -lnwcblas -lnwclapack  -lnwcblas   -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/2.1.1/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi      -lpthread   
nwchem is built

Thanks!
Matt

Forum Vet

10:33:43 AM PDT - Tue, Jul 25th 2017
Matt I have tried to reproduce your environment on my Mac sierra 10.12.6, but, even though my link command seems to the same as yours, I am not seeing any segfault. Did you recompile from scratch after applying the patch (e.g. make realclean)? Could you send the output of the command otool -L $NWCHEM_TOP/bin/MACX64/nwchem

Just Got Here

4:30:07 AM PDT - Wed, Jul 26th 2017
I hadn't done make realclean, but I had tried a fresh install by unpacking the source code in a new directory, applying the patches, and compiling. I just performed real makeclean and recompiled, and the problem appears to be solved. Very strange. Thanks for your help.

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