ABINIT Discussion Forums

Hi,
When I try to install on my computer(ubuntu 10.10,gfortran4.4 gcc4.4 g++4.4,openmpi1.4.3),some problems came up.
I installed openmpi at /home/pc/openmpi
and used export LD_LIBRARY_PATH=/home/pc/openmpi/lib
then used ./configure --enable-mpi --enable-64bit-flags --with-mpi-prefix=/home/pc/openmpi to configure
then sudo make,but errors came up:
configure: finding C compiler
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... configure: error: in `/home/pc/Downloads/abinit-6.6.1/plugins/netcdf/netcdf-4.1.1':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.
make[4]: *** [configure-stamp] Error 1
make[4]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/netcdf'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/netcdf'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/pc/Downloads/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

Hello Zjuer,

you seem to be in trouble to compile the netcdf plugin; the error message is somewhat misleading - it's not the main config.log that contains the relevant information but the one in plugins/netcdf/netcdf-4.1.1/config.log. Would you be so kind to save a copy of it and post here for inspection.

You have another option to compile Abinit with netcdf support: install Ubuntu netcdf package, reconfigure Abinit to detect it - and not to compile the "fallback"

So install the netcdf 4 devel, cleanup your Abinit tree and reconfigure with ...
And don't forget to run the testsuite after if compilation is successful. If it fails, a copy of the main config.log, config.h and src/98_main/Makefile would help me to find out.

Kind regards,

Alain

Hello Alain,
Thank you for your help. I have posted the plugins/netcdf/netcdf-4.1.1/config.log, please have a look at it. Thanks
I also tried
sudo apt-get install libnetcdf-dev
make distclean
configure ... the one you mentioned earlier
make, but something else came up,
mkdir tmp
cd etsf_io-1.0.3 && \
F77="/home/pc/openmpi/bin/mpif90 -m64" \
FFLAGS="-m64 -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse" \
F90="/home/pc/openmpi/bin/mpif90 -m64" \
F90FLAGS="-m64 -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse" \
FC="/home/pc/openmpi/bin/mpif90 -m64" \
FCFLAGS="-m64 -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse" \
./configure \
--prefix=/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io/tmp \
--with-moduledir=/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io/tmp/include \
--with-netcdf-module-path=`echo "-I/usr/include" | sed -e "s/-I//"` \
--with-netcdf-ldflags=`echo "-lnetcdff -lnetcdf" | sed -e "s/-lnetcdf//"` \

configure: error: unrecognized option: -lnetcdf
Try `./configure --help' for more information.
make[4]: *** [configure-stamp] Error 1
make[4]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/pc/Downloads/abinit-6.6.1'
make: *** [all] Error 2
The main config.log, config.h and src/98_main/Makefile are enclosed.

Best regards,

zjuer

Hmmm ... tiny bug, it will be corrected in 6.6.2

Meanwhile, you can apply the following patch to the <root>/plugins/etsf_io/etsf_io.mk file
After that, you can go on with the make but as you're close to the beginning of the compilation, it's probably advisable to clean, reconfigure and make again.

Alain

@Alain: a "make clean" in plugins/etsf_io/ will be enough in this case.

Hello Alain,
I don't know how to use your patch correctly. I tried to add your patch at the end of etsf_io.mk, the entire etsf_io.mk is attached, but it does not work, and some new problems show up. Could you give me a hand? Thanks.

Best regards,

zjuer

make[4]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/linalg'
if test -d tmp ; then find tmp -type f -exec mv {} . \; ; rm -rf tmp ; fi
make[3]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/linalg'
Making all in etsf_io
make[3]: Entering directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
make -f ../../plugins/etsf_io/etsf_io.mk
make[4]: Entering directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
../../plugins/etsf_io/etsf_io.mk:54: *** target pattern contains no `%'. Stop.
make[4]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/pc/Downloads/abinit-6.6.1'
make: *** [all] Error 2

Save the patch to a file, let's say etsf_io.patch, and do the following:

Hello pouillon,
Thanks for your help. When I try to patch according to your suggestion some problems appear. Could you tell me how to deal with the problem? Thank you.

pc@uiuc:~/Downloads/abinit-6.6.1$ patch -p0 < new.patch
patching file plugins/etsf_io/etsf_io.mk
Hunk #1 FAILED at 36.
1 out of 1 hunk FAILED -- saving rejects to file plugins/etsf_io/etsf_io.mk.rej


new.patch:
=== modified file plugins/etsf_io/etsf_io.mk
--- plugins/etsf_io/etsf_io.mk 2010-09-04 11:11:20 +0000
+++ plugins/etsf_io/etsf_io.mk 2011-03-17 20:29:16 +0000
@@ -36,7 +36,7 @@
--prefix=$(PWD)/tmp \
--with-moduledir=$(PWD)/tmp/include \
--with-netcdf-module-path=`echo "$(lib_netcdf_incs)" | sed -e "s/-I//"` \
- --with-netcdf-ldflags=`echo "$(lib_netcdf_libs)" | sed -e "s/-lnetcdf//"` \
+ --with-netcdf-ldflags=`echo "$(lib_netcdf_libs)" | sed -e "s/-lnetcdf[f_]*//g"` \
$(CFGFLAGS_ETSF_IO)
touch configure-stamp

Hello Zjuer,

Assuming that you're still working in the same directory structure as before ...
then edit etsf_io.mk to change the end of 39th line from to

Alain

Hello Alain and Pouillon,
Thank you two wery much. The compilation is successful now.

Best regards.

Zjuer

Hello Alain and Pouillon,
I am sorry to trouble you again. Today I try to recompile abinit6.6.1 in order to change the installation directory. But I failed. Then I reinstalled the operating system and tried again and I got the error information which is similar with last time. Since I have changed the etsf_io.mk file as before, I can not find out what is wrong this time. The config.log inetsf_io-1.0.3 is enclosed. Could you have a look at this problem? Thanks.

Best regards,

Zjuer

cd etsf_io-1.0.3 && \
F77="/home/pc/openmpi/bin/mpif90 -m64" \
FFLAGS="-m64 -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse" \
F90="/home/pc/openmpi/bin/mpif90 -m64" \
F90FLAGS="-m64 -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse" \
FC="/home/pc/openmpi/bin/mpif90 -m64" \
FCFLAGS="-m64 -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse" \
./configure \
--prefix=/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io/tmp \
--with-moduledir=/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io/tmp/include \
--with-netcdf-module-path=`echo "-I/usr/include" | sed -e "s/-I//"` \
--with-netcdf-ldflags=`echo "-lnetcdff -lnetcdf" | sed -e "s/-lnetcdf[f_]*//g"` \

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for Fortran compiler default output file name... a.out
checking whether the Fortran compiler works... configure: error: cannot run Fortran compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.
make[4]: *** [configure-stamp] Error 1
make[4]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins/etsf_io'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/pc/Downloads/abinit-6.6.1/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/pc/Downloads/abinit-6.6.1'
make: *** [all] Error 2

In the enclosed config.log:

configure:2433: checking whether the Fortran compiler works
configure:2443: ./a.out
./a.out: error while loading shared libraries: libmpi_f90.so.0: cannot open shared object file: No such file or directory
configure:2446: $? = 127
configure:2455: error: cannot run Fortran compiled programs.

i.e. a program - a.out - compiled with mpif90 cannot be executed because the libmpi_f90.so dynamic library cannot be found. Very probably because the LD_LIBRARY_PATH doesn't contain the path to your openmpi libraries. Use where /xxx point to the directory of your openmpi libs

Kind regards,

Alain

Hello Alain,
I have rechecked the problem of LD_LIBRARY_PATH, and verified with echo${LD_LIBRARY_PATH}, but the problem is still the same.

Best regards,

Zjuer

Hello Alain,
It works again after use --with-dft-flavor="none" to configure and make it. Thank you.

Best regards,

Zjuer