ABINIT Discussion Forums

When I try to install abinit on the cluster (RedHat Enterprise Linux 5 x86_64, gcc 4.5.2, intel 10.1)
I have tried:
1. ./configure --prefix...
2. make FC=gfortran, then error came up as the following

make[7]: Entering directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
echo '! NetCDF-3.' > netcdf.inc
cat ../fortran/netcdf3.inc >> netcdf.inc
make all-am
make[8]: Entering directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -DNDEBUG -DpgiFortran -g -O2 -MT fort-attio.lo -MD -MP -MF $depbase.Tpo -c -o fort-attio.lo fort-attio.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -DNDEBUG -DpgiFortran -g -O2 -MT fort-attio.lo -MD -MP -MF .deps/fort-attio.Tpo -c fort-attio.c -o fort-attio.o
In file included from fort-attio.c：7 :
ncfortran.h:26:42: error：NF_INT_IS_C_... not defined：No such file or directory
fort-attio.c: In function ‘NF_INT_cfF’:
fort-attio.c:13: error：expected declaration specifiers before ‘NF_INTEGER’
fort-attio.c:20: error：expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:121: error：expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:133: error：expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:141: error：expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:148: error：expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:148: error：expected ‘{’ at end of input
make[8]: *** [fort-attio.lo] error 1
make[8]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
make[7]: *** [all] error 2
make[7]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
make[6]: *** [all-recursive] error 1
make[6]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1'
make[5]: *** [all] error 2
make[5]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1'
make[4]: *** [build-stamp] error 2
make[4]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf'
make[3]: *** [package-ready] error 2
make[3]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf'
make[2]: *** [all-recursive] error 1
make[2]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins'
make[1]: *** [all-recursive] error 1
make[1]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1'
make: *** [all] error 2

I don't know how to solve this problem. Does anyone know what the problem is? Thanks

I have thought there are some thing wrong with the netcdf in the plugins directory, then I download a netcdf package form the web page http://www.unidata.ucar.edu/software/netcdf/ and install it, then i try --with-netcdf=... while configuring abinit, but it doesn't work!
Thanks for your kindness help!

Dear Zidan,

From your config.log ...

configure:10801: gcc --version >&5
gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)

i.e. 4.1.2 = old stuff = unsupported. I would suggest to adapt your environment to the gcc-4.5.2 that you mentioned (i.e. PATH and LD_LIBRARY_PATH) and configure Abinit with a proper ../configure ... FC=/path_to_4.5.2/bin/gfortran CC=/path_to_4.5.2/bin/gcc CXX=/path_to_4.5.2/bin/g++

Kind regards,

Alain

Alain_Jacques wrote:Dear Zidan,

From your config.log ...

configure:10801: gcc --version >&5
gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)

i.e. 4.1.2 = old stuff = unsupported. I would suggest to adapt your environment to the gcc-4.5.2 that you mentioned (i.e. PATH and LD_LIBRARY_PATH) and configure Abinit with a proper ../configure ... FC=/path_to_4.5.2/bin/gfortran CC=/path_to_4.5.2/bin/gcc CXX=/path_to_4.5.2/bin/g++

Kind regards,

Alain

Dear Alain
Thanks for your kindness help
Although I didn't add "FC=/path_to_4.5.2/bin/gfortran CC=/path_to_4.5.2/bin/gcc CXX=/path_to_4.5.2/bin/g++" when I "./configure", but I had use them when "make " .
Now I have tried the way you suggested, but the "make" process interrupted too

/bin/sh ../libtool --tag=FC --mode=link /vol5/home/simg/software/local/gcc-4.5.2/bin/gfortran -I../libsrc -I. -ffree-form -g -ffree-line-length-none -Wstrict-aliasing=2 -O2 -mtune=native -march=native -mfpmath=sse -o libnetcdff90.la typeSizes.lo netcdf.lo
libtool: link: ar cru .libs/libnetcdff90.a typeSizes.o netcdf.o
libtool: link: ranlib .libs/libnetcdff90.a
libtool: link: ( cd ".libs" && rm -f "libnetcdff90.la" && ln -s "../libnetcdff90.la" "libnetcdff90.la" )
make[8]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/f90'
make[7]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/f90'
Making all in fortran
make[7]: Entering directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
echo '! NetCDF-3.' > netcdf.inc
cat ../fortran/netcdf3.inc >> netcdf.inc
make all-am
make[8]: Entering directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CC --mode=compile /vol5/home/simg/software/local/gcc-4.5.2/bin/gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -DNDEBUG -DpgiFortran -g -O2 -mtune=native -march=native -mfpmath=sse -MT fort-attio.lo -MD -MP -MF $depbase.Tpo -c -o fort-attio.lo fort-attio.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /vol5/home/simg/software/local/gcc-4.5.2/bin/gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -DNDEBUG -DpgiFortran -g -O2 -mtune=native -march=native -mfpmath=sse -MT fort-attio.lo -MD -MP -MF .deps/fort-attio.Tpo -c fort-attio.c -o fort-attio.o
In file included from fort-attio.c:7:0:
ncfortran.h:26:42: Fatal error：NF_INT_IS_C_... not defined：no such file or directory
compilling interrupted。
make[8]: *** [fort-attio.lo] error 1
make[8]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
make[7]: *** [all] error 2
make[7]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1/fortran'
make[6]: *** [all-recursive] error 1
make[6]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1'
make[5]: *** [all] error 2
make[5]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1'
make[4]: *** [build-stamp] error 2
make[4]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf'
make[3]: *** [package-ready] error 2
make[3]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins/netcdf'
make[2]: *** [all-recursive] error 1
make[2]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1/plugins'
make[1]: *** [all-recursive] error 1
make[1]: Leaving directory `/vol5/home/simg/software/abinit-6.6.1'
make: *** [all] error 2

Did you "make clean" before the configure step?

Alain_Jacques wrote:Did you "make clean" before the configure step?

I delete the abinit-6.6.1 folder and untar the abinit-6.6.1 package, and then "./configure --prefix=/vol5/home/simg/software/abinit/ FC=/vol5/home/simg/software/local/gcc-4.5.2/bin/gfortran CC=/vol5/home/simg/software/local/gcc-4.5.2/bin/gcc CXX=/vol5/home/simg/software/local/gcc-4.5.2/bin/g++" and "make"

two sugestions ...
x use --enable-64bit-flags
x you seem to have a netcdf package already installed - probably from RH repositories. Would you please check this with a If you're allowed to do so, can you remove it for the moment - at least the netcdf-devel package?

Alain

I have tried the two suggestions you gave, but the "make" process interrupted at the same place as before! I think there are something wrong with the netcdf compilling, but i don't know how to fix it! Thinks!

Zidan

If you have a NetCDF package already installed - or can install one, I suggest you to do so instead of trying to build it within Abinit. This will likely work much better.

Yes, I have installed netcdf, and I try to install abinit again, with :
./configure --prefix=/vol5/home/simg/software/abinit/ FC=/vol5/home/simg/software/local/gcc-4.5.2/bin/gfortran CC=/vol5/home/simg/software/local/gcc-4.5.2/bin/gcc CXX=/vol5/home/simg/software/local/gcc-4.5.2/bin/g++ --with_netcdf_incs="-I/vol5/home/simg/software/library/netcdf/include" --with_netcdf_libs="-L/vol5/home/simg/software/library/netcdf/lib/netcdf -lnetcdf"
and the configure feedback message shows that the external netcdf doesn't work:
==============================================================================
=== Connectors / Fallbacks ===
==============================================================================

checking whether MPI is usable... no
checking whether to build MPI code... no
checking whether to activate GPU support... no
checking for the requested transferable I/O support... etsf_io
checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking for Fortran module includes... unknown
configure: error: external netcdf support does not work

How can I make it work? thanks!

Zidan

Hello Zidan,

Question 1: do you have a RH installed netcdf package; check with rpm -qa as mentioned earlier. If yes, please report the name of the package - there are several sources of netcdf on RH distribution.

Question 2: Do you have a file named /vol5/home/simg/software/library/netcdf/lib/libnetcdff.* - * can be "a" (i.e. static) or "so. ..." (dynamic lib). You have to choose either to build a 32bit or 64bit Abinit and combine with the same kind of libraries i.e. mixing doesn't work. If yes, check with a "file libnetcdff.so" (adapt libnetcdff.so to your case) that it is a 64bit library. And if yes again, cleanup the build directory and change the relevant part in your configure options to --enable-64bit-flags --with_netcdf_libs="-L/vol5/home/simg/software/library/netcdf/lib/netcdf -lnetcdff -lnetcdf".

Kind regards,

Alain

Looks to me as if Abinit's configure is unable to find the "netcdf.mod" file. Just find where it is and call configure again adding the following at the end:

This should solve your problem.

Alain_Jacques wrote:
Question 1: do you have a RH installed netcdf package; check with rpm -qa as mentioned earlier. If yes, please report the name of the package - there are several sources of netcdf on RH distribution.

Question 2: Do you have a file named /vol5/home/simg/software/library/netcdf/lib/libnetcdff.* - * can be "a" (i.e. static) or "so. ..." (dynamic lib). You have to choose either to build a 32bit or 64bit Abinit and combine with the same kind of libraries i.e. mixing doesn't work. If yes, check with a "file libnetcdff.so" (adapt libnetcdff.so to your case) that it is a 64bit library. And if yes again, cleanup the build directory and change the relevant part in your configure options to --enable-64bit-flags --with_netcdf_libs="-L/vol5/home/simg/software/library/netcdf/lib/netcdf -lnetcdff -lnetcdf".

Question 1: There is no RH installed netcdf package,when I print "rpm -qa |grep netcdf", nothing appeared on the screen.

Question 2: I do have the file you mentioned, and in that folder I can see these files: "libnetcdf.a libnetcdf_c++.a libnetcdf_c++.la libnetcdf.la pkgconfig".

I re-configure with:


it's still doesn't work:

checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking for Fortran module includes... unknown
configure: error: external netcdf support does not work

I tried both in our lab cluster or in Tianjin Super Computational Center, The results are the same!

pouillon wrote:Looks to me as if Abinit's configure is unable to find the "netcdf.mod" file. Just find where it is and call configure again adding the following at the end:

Code: Select all

CPPFLAGS_EXTRA="-I/path/of/netcdf_mod" FCFLAGS_EXTRA="-I/path/of/netcdf_mod"

There is no file called "netcdf.mod" but do have other files named "netcdf.mk" or "netcdf.pc" or"netcdf.pc.in"

I can successfully install abinit with

There is no file called "netcdf.mod" but do have other files named "netcdf.mk" or "netcdf.pc" or"netcdf.pc.in"

Of course, you won't find such a file inside the source tree of Abinit. If you installed NetCDF fully, there has to be a "netcdf.mod" file somewhere. You might find it using "rpm -q --filesbypkg".

Dear Alain and Pouillon:
Thanks very much for your kindness help, finally I have successfully installed abinit package and it works well!
Kind regards!

Zidan