Compiling NWChem 6.6 on openSUSE42.1


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Clicked A Few Times
2:45:29 PM PST - Tue, Dec 15th 2015
Hello,

I following the documentation availible to compile NWChem on openSUSE and keep getting a "**No rule to make target 'nwchem_config' in the first make step.

Here are my environment settings:

export NWCHEM_TOP=/home/franksus/Desktop/nwchem/nwchem-6.6/
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export USE_64TO32=y
export BLAS_SIZE=4
export BLASOPT="-lopenblas -lpthread -lrt"
export PATH=/usr/lib64/mpi/gcc/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/usr/lib64/mpi/gcc/openmpi/lib64:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH


Here are my make settings

make nwchem_config NWCHEM_MODULES="all python"
make 64_to_32
make


Here is what is see:

ranksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6> make nwchem_config NWCHEM_MODULES="all python"
make: *** No rule to make target 'nwchem_config'. Stop.

I have also tried changing the environment settings as

export USE_MPI=y
export LIBMPI="-lmpich -lopa -lmpl -lpthread -lmpichf90 -lfmpich -lmpich"
export MPI_LIB=v/usr/local/mpich2.141p1/lib
export MPI_INCLUDE=/usr/local/mpich2.141p1/include/



Any ideas on what I can do? Seems like a simple fix, but I am a linux n00bs..

Forum Vet
7:22:09 PM PST - Tue, Dec 15th 2015
You are in the wrong directory. Please execute the command

cd $NWCHEM_TOP/src

Clicked A Few Times



ranksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> make
test \! -f 64_to_32 -o \! -f 32_to_64 || rm -f 64_to_32 32_to_64
test -d /home/franksus/Desktop/nwchem/nwchem-6.6//lib/LINUX64 || mkdir -p /home/franksus/Desktop/nwchem/nwchem-6.6//lib/LINUX64
test -d /home/franksus/Desktop/nwchem/nwchem-6.6//bin/LINUX64 || mkdir -p /home/franksus/Desktop/nwchem/nwchem-6.6//bin/LINUX64
./util/util_nwchem_version.bash
which: no svn in (/usr/lib64/openmpi/bin/:/usr/lib64/mpi/gcc/openmpi/bin:/usr/lib64/mpi/gcc/openmpi/bin:/home/franksus/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games)
Making libraries in tools
make[1]: Entering directory '/home/franksus/Desktop/nwchem/nwchem-6.6/src/tools'
rm -f ./*.FC.stamp
echo "" > gfortran.FC.stamp
rm -f ./*.CC.stamp
echo "" > cc.CC.stamp
rm -rf build install
rm -f ./*.DIR.stamp
echo "" > ga-5-4.DIR.stamp

      • Configuring Parallel Tools ****

which: no svn in (/usr/lib64/openmpi/bin/:/usr/lib64/mpi/gcc/openmpi/bin:/usr/lib64/mpi/gcc/openmpi/bin:/home/franksus/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games)
../ga-5-4/configure --prefix=/home/franksus/Desktop/nwchem/nwchem-6.6/src/tools/install --with-tcgmsg --with-mpi=-I/usr/local/mpich2.141p1/include -Lv/usr/local/mpich2.141p1/lib -lmpich -lopa -lmpl -lpthread -lmpichf90 -lfmpich -lmpich --enable-peigs --enable-underscoring --disable-mpi-tests --without-scalapack --without-lapack --with-blas4=-lopenblas -lpthread -lrt --with-mpi-ts CC=cc CXX=g++ F77=gfortran ARMCI_DEFAULT_SHMMAX_UBOUND=131072
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for TARGET base (64bit-ness checked later)... LINUX
checking whether we think this system is what we call SYSV... yes
checking whether we are cross compiling... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Detected VPATH build
configure:
configure: C compiler
configure:
checking for style of include used by make... GNU
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for C compiler vendor... gnu
checking whether a simple C MPI program compiles... no
configure: error: in `/home/franksus/Desktop/nwchem/nwchem-6.6/src/tools/build':
configure: error: could not compile simple C MPI program
See `config.log' for more details
GNUmakefile:561: recipe for target 'build/config.status' failed
make[1]: *** [build/config.status] Error 1
make[1]: Leaving directory '/home/franksus/Desktop/nwchem/nwchem-6.6/src/tools'
GNUmakefile:103: recipe for target 'libraries' failed
make: *** [libraries] Error 1

11:47:52 AM PST - Wed, Dec 16th 2015

Forum Vet
2:52:44 PM PST - Wed, Dec 16th 2015
MPI
checking whether a simple C MPI program compiles... no
configure: error: in `/home/franksus/Desktop/nwchem/nwchem-6.6/src/tools/build':
configure: error: could not compile simple C MPI program
See `config.log' for more details
GNUmakefile:561: recipe for target 'build/config.status' failed
make[1]: *** [build/config.status] Error 1
make[1]: Leaving directory '/home/franksus/Desktop/nwchem/nwchem-6.6/src/tools'
GNUmakefile:103: recipe for target 'libraries' failed
make: *** [libraries] Error 1


This is a problem.
Do you have a working MPI installation?
Please send the output of the command


which mpif90
mpif90 -show

Clicked A Few Times
3:00:37 PM PST - Wed, Dec 16th 2015
Yes, I believe I have mpif90, but maybe I used the wrong environment variables? Here are the results

Edit: Don't think this makes a difference, but I am using Virtualbox; openSUSE installed without any problems though.


franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> which mpif90
/usr/lib64/mpi/gcc/openmpi/bin/mpif90                                                                                                                
franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> mpif90 -show
gfortran -I/usr/lib64/mpi/gcc/openmpi/include -pthread -I/usr/lib64/mpi/gcc/openmpi/lib64 -Wl,-rpath -Wl,/usr/lib64/mpi/gcc/openmpi/lib64 -Wl,--enable-new-dtags -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_usempi -lmpi_mpifh -lmpi

Forum Vet
3:17:40 PM PST - Wed, Dec 16th 2015
Please unset MPI_INCLUDE, MPI_LIB and LIBMPI and restart the compilation

Clicked A Few Times
4:30:52 PM PST - Wed, Dec 16th 2015
The unset fixes worked, but now there is a new problem. Problem is along the lines of "cannot find -lopenblas". This looks similar to the problem the patch fixed, but I'm not sure.

Here is the last few lines of the output

make[1]: Leaving directory '/home/franksus/Desktop/nwchem/nwchem-6.6/src'
gfortran  -Wl,--export-dynamic  -L/home/franksus/Desktop/nwchem/nwchem-6.6//lib/LINUX64 -L/home/franksus/Desktop/nwchem/nwchem-6.6//src/tools/install/lib64   -o /home/franksus/Desktop/nwchem/nwchem-6.6//bin/LINUX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 -lopenblas -lpthread -lrt  -lnwclapack  -lnwcblas   -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_usempi -lmpi_mpifh -lmpi  -lnwcutil -lpython2.7 -lpthread -ldl -lutil -lm  -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic  
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lopenblas
collect2: error: ld returned 1 exit status
GNUmakefile:33: recipe for target 'all' failed
make: *** [all] Error 1

Forum Vet
5:34:01 PM PST - Wed, Dec 16th 2015
openblas-devel rpm
Have you installed the openblas-devel rpm?
What is the output of the commands
rpm -q -l openblas-devel
zypper info openblas-devel

By the way, have you typed
make 64_to_32
prior to
make
?

Clicked A Few Times
6:30:11 PM PST - Wed, Dec 16th 2015
Quote:Edoapra Dec 16th 4:34 pm
Have you installed the openblas-devel rpm?


Yes of course. Here is the output of the commands


franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> rpm -q -l openblas-devel
/usr/lib64/cmake
/usr/lib64/cmake/openblas
/usr/lib64/cmake/openblas/OpenBLASConfig.cmake
/usr/lib64/libopenblas.so
/usr/share/doc/packages/openblas-devel
/usr/share/doc/packages/openblas-devel/Changelog.txt
/usr/share/doc/packages/openblas-devel/GotoBLAS_00License.txt
/usr/share/doc/packages/openblas-devel/GotoBLAS_01Readme.txt
/usr/share/doc/packages/openblas-devel/GotoBLAS_02QuickInstall.txt
/usr/share/doc/packages/openblas-devel/GotoBLAS_03FAQ.txt
/usr/share/doc/packages/openblas-devel/GotoBLAS_04FAQ.txt
/usr/share/doc/packages/openblas-devel/GotoBLAS_05LargePage.txt
/usr/share/doc/packages/openblas-devel/GotoBLAS_06WeirdPerformance.txt
/usr/share/doc/packages/openblas-devel/LICENSE
/usr/share/doc/packages/openblas-devel/README.SUSE
/usr/share/doc/packages/openblas-devel/README.md
franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> 
franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> 
franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> zypper info openblas-devel
Loading repository data...
Reading installed packages...


Information for package openblas-devel:
---------------------------------------
Repository: Main Repository (OSS)
Name: openblas-devel
Version: 0.2.14-4.5
Arch: x86_64
Vendor: openSUSE
Installed: Yes
Status: up-to-date
Installed Size: 37.6 KiB
Summary: Development headers and libraries for OpenBLAS
Description: 
  OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
  This package contains the development libraries and headers for OpenBLAS.



When I type make 64_to_32 I get (which I did before make):

franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> make 64_to_32
make: '64_to_32' is up to date.




Should I try installing openblas-devel-headers instead?? Or just wipe everything and start again from scratch?

Forum Vet
11:07:17 AM PST - Thu, Dec 17th 2015
No need for openblas-devel-headers
Have you installed the patch Tools_lib64.patch.gz as explained in
http://nwchemgit.github.io/Special_AWCforum/sp/id6606

?

Clicked A Few Times
12:59:37 PM PST - Thu, Dec 17th 2015
Quote:Edoapra Dec 17th 10:07 am
No need for openblas-devel-headers
Have you installed the patch Tools_lib64.patch.gz as explained in
http://nwchemgit.github.io/Special_AWCforum/sp/id6606

?


Yes, I applied the patch tools. I recompiled and again, I found the same error. Maybe my environment settings are wrong?

Forum Vet
1:01:36 PM PST - Thu, Dec 17th 2015
Could you upload $NWCHEM_TOP/src/tools/build/config.log to a website of your choice?

Clicked A Few Times
1:12:22 PM PST - Thu, Dec 17th 2015
Quote:Edoapra Dec 17th 12:01 pm
Could you upload $NWCHEM_TOP/src/tools/build/config.log to a website of your choice?


You got it. Below is the pastebin url

http://pastebin.ca/3290492

Forum Vet
1:44:38 PM PST - Thu, Dec 17th 2015
This log does not look good at all.
It is the result of wrong MPI_ settings.
Could you please unset MPI_INCLUDE, LIBMPI, MPI_LIB (as suggested yesterday)

Clicked A Few Times
1:58:13 PM PST - Thu, Dec 17th 2015
Quote:Edoapra Dec 17th 12:44 pm
This log does not look good at all.
It is the result of wrong MPI_ settings.
Could you please unset MPI_INCLUDE, LIBMPI, MPI_LIB (as suggested yesterday)



I thought I did.... Silly question, but is there a specific order for the unset command? Here is what I am doing:

Environment
export NWCHEM_TOP=/home/franksus/Desktop/nwchem/nwchem-6.6/
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export USE_64TO32=y
export BLAS_SIZE=4
export BLASOPT="-lopenblas -lpthread -lrt"
export PATH=/usr/lib64/mpi/gcc/openmpi/bin:$PATH 
export LD_LIBRARY_PATH=/usr/lib64/mpi/gcc/openmpi/lib64:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH
unset MPI_INCLUDE 
unset MPI_LIB
unset LIBMPI


make 
cd %NWCHEM_TOP/src
make nwchem_config NWCHEM_MODULES="all python"
make 64_to_32
make


I appreciate your patience with me. Recompiling again..

Ninaj edit: Forgot to add cd

Clicked A Few Times
3:33:48 PM PST - Thu, Dec 17th 2015
Again, same error.

I decided to remove and reinstall openblas-devel. Here is what I see, something is not right..


franksus@linux-94w6:~/Desktop/nwchem/nwchem-6.6/src> sudo zypper install openblas-devel
Loading repository data...
Reading installed packages...
Resolving package dependencies...

Problem: openblas-devel-0.2.14-4.5.x86_64 requires openblas-devel-headers = 0.2.14, but this requirement cannot be provided
  uninstallable providers: openblas-devel-headers-0.2.14-4.6.noarch[download.opensuse.org-oss]
 Solution 1: do not install openblas-devel-0.2.14-4.5.x86_64
 Solution 2: break openblas-devel-0.2.14-4.5.x86_64 by ignoring some of its dependencies


I can't remember if the first time around I tried solution 2 and ignored some of the dependencies. This could be at fault?

I will try to recompile with openblas-devel-headers instead. I'll post here what I get.


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