install 6.6.2

[zjuer]

Hello,
when I install 6.6.2 on my computer, there are some errors show up. Could anyone help me out? Thanks.

Making all in 10_defs
make[3]: Entering directory `/home/pc/Downloads/abinit-6.6.2/src/10_defs'
/usr/lib64/openmpi/bin/mpif90 -m64 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -ffree-form -J/home/pc/Downloads/abinit-6.6.2/src/mods -O2 -mtune=native -march=native -mfpmath=sse -m64 -g -ffree-line-length-none -Wstrict-aliasing=2 -c -o defs_basis.o defs_basis.F90
/usr/lib64/openmpi/bin/mpif90 -m64 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -ffree-form -J/home/pc/Downloads/abinit-6.6.2/src/mods -O2 -mtune=native -march=native -mfpmath=sse -m64 -g -ffree-line-length-none -Wstrict-aliasing=2 -c -o defs_aimfields.o defs_aimfields.F90
/usr/lib64/openmpi/bin/mpif90 -m64 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -ffree-form -J/home/pc/Downloads/abinit-6.6.2/src/mods -O2 -mtune=native -march=native -mfpmath=sse -m64 -g -ffree-line-length-none -Wstrict-aliasing=2 -c -o defs_aimprom.o defs_aimprom.F90
/usr/lib64/openmpi/bin/mpif90 -m64 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -ffree-form -J/home/pc/Downloads/abinit-6.6.2/src/mods -O2 -mtune=native -march=native -mfpmath=sse -m64 -g -ffree-line-length-none -Wstrict-aliasing=2 -c -o defs_parameters.o defs_parameters.F90
/usr/lib64/openmpi/bin/mpif90 -m64 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -ffree-form -J/home/pc/Downloads/abinit-6.6.2/src/mods -O2 -mtune=native -march=native -mfpmath=sse -m64 -g -ffree-line-length-none -Wstrict-aliasing=2 -c -o defs_datatypes.o defs_datatypes.F90
defs_datatypes.F90:86.34:
use BigDFT_API, only : atoms_data 1
Fatal Error: Can't open module file 'bigdft_api.mod' for reading at (1): No such file or directory
make[3]: *** [defs_datatypes.o] Error 1
make[3]: Leaving directory `/home/pc/Downloads/abinit-6.6.2/src/10_defs'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/pc/Downloads/abinit-6.6.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/pc/Downloads/abinit-6.6.2'
make: *** [all] Error 2

[pouillon]

Try to configure with the following option:

Code: Select all

../configure --with-dft-flavor="libxc+wannier90"

[Alain_Jacques]

Hi zjuer,

It sounds fishy ... you should have a -I pointing to the plugins/bigdft directory in the invocations of src/10_defs. Would you please tell me if you have the module compiled and installed? You should find 2 copies: in plugins/bigdft/bigdft-1.2.0.2/src/bigdft_api.mod and in plugins/bigdft/bigdft_api.mod. Do you find them?

Kind regards,

Alain

[zjuer]

Hello Alain,
I have recompiled abinit662. but there is no bigdft_api.mod exist. Last time I also encountered the same problem and I tried to cope a bigdft_api.mod from other machine, but it didn't work as well. I don't know what's the problem is? Do you have any idea? Thanks

Best regards,

Zjuer

[zjuer]

Try to configure with the following option:

Code: Select all

../configure --with-dft-flavor="libxc+wannier90"

Hello pouillon,
I also compiled abinit662 following your suggestion, but it still not succeed.

[Lastik2004]

Hello,
I've realized similar confusing problem, where no 'bigdft_api.mod' is detected on the machine.
When the last suggestion

../configure --with-dft-flavor="libxc+wannier90"

has been tried the "make" crushed with following message:
##################################################
cc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../.. -lgfortran -lm
../../src/67_common/lib67_common.a(mlwfovlp.o): In function `mlwfovlp':
/home/spodi/SimulCodes/abinit-6.6.2/src/67_common/mlwfovlp.F90:1044: undefined reference to `wannier_run_'
../../src/67_common/lib67_common.a(mlwfovlp_setup.o): In function `mlwfovlp_setup':
/home/spodi/SimulCodes/abinit-6.6.2/src/67_common/mlwfovlp_setup.F90:211: undefined reference to `wannier_setup_'
collect2: ld returned 1 exit status
make[3]: *** [abinit] Error 1
make[3]: Leaving directory `/home/spodi/SimulCodes/abinit-6.6.2/src/98_main'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/spodi/SimulCodes/abinit-6.6.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/spodi/SimulCodes/abinit-6.6.2'
make: *** [all] Error 2
#####################################################
It would be great if somebody could give us a hint what is going on there.
Regards,
Anatoliy Senyshyn aka Lastik2004

[Alain_Jacques]

Hi Lastik2004,

Refering to your config.log ...

configure:34043: using tarball repository /root/.abinit/tarballs
configure:34055: WARNING: no 'patch' command available
configure:34058: WARNING: disabling BigDFT (requires patch)
configure:34063: WARNING: disabling Wannier90 (requires patch)
configure:34234: checking for a source tarball of LINALG

The patch utility is missing and, as a consequence, plugins requiring to be patched during Abinit compilation are disabled - I agree that the logic behind the disable is broken (Yann ... up to you). I suggest to use Suse repositories to install patch; it's certainly available - it's a classic tool. Then cleanup the build directory, reconfigure and make again.

Kind regards,

Alain

[zjuer]

Hello Alain,
I attached my config.log ,could you have a look to see what's the problem with it? Thank you.

Best,

zjuer

[Alain_Jacques]

Hello Zjuer,

Look in config.log ...

configure:34043: using tarball repository /home/pc/.abinit/tarballs
configure:34055: WARNING: no 'patch' command available
configure:34058: WARNING: disabling BigDFT (requires patch)
configure:34063: WARNING: disabling Wannier90 (requires patch)

Same story for you: no patch installed on your system. So configure tries to disable all options that will require patch and fails to do it cleanly. Please install patch from Fedora repositories ... probably with a plain

Code: Select all

sudo yum install patch

Then cleanup Abinit build attempts, reconfigure and make - and it should compile smoothly.

Kind regards,

Alain

[zjuer]

Hello Zjuer,

Look in config.log ...

configure:34043: using tarball repository /home/pc/.abinit/tarballs
configure:34055: WARNING: no 'patch' command available
configure:34058: WARNING: disabling BigDFT (requires patch)
configure:34063: WARNING: disabling Wannier90 (requires patch)

Same story for you: no patch installed on your system. So configure tries to disable all options that will require patch and fails to do it cleanly. Please install patch from Fedora repositories ... probably with a plain

Code: Select all

sudo yum install patch

Then cleanup Abinit build attempts, reconfigure and make - and it should compile smoothly.

Kind regards,

Alain

Hello Alian,
According to you suggestion I compiled abinit successfully. But when I try to run abinit there is a fault like "error while loading shared libraries: libmpi_f90.so.0: cannot open shared object file: No such file or directory"
Is it because my wrong configure parameter? I used ./configure --enable-mpi --enable-64bit-flags=yes --with-mpi-prefix=/usr/lib64/openmpi to configure. Thanks.

Best,

zjuer

[Alain_Jacques]

Looking at your mpi-prefix option, I assume that libmpi*.so file reside in /usr/lib64/openmpi/lib/ ... right?
If Abinit doesn't find its dynamic libraries, i.e. a

Code: Select all

ldd abinit

returns one or several "not found" libs them give it a clue by setting ...

Code: Select all

export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH

Now the ldd should return the path to all dynamic libraries.

Alain

[zjuer]

Hello Alain,
Thanks your suggestion. It work fine up to now.

Best,

Zjuer