Error during installation of YAMBO v4.5.0

[soumyadeepghosh35]

Dear All,
I found some error during serial installing of YAMBO 4.5.0 in RHEL v7.2. The source code compiled successfully in Ubuntu-16.04. So problem lies in RHEL system. PC architecture: Linux hghosh.novalocal 3.10.0-327.el7.x86_64 #1 SMP Thu Oct 29 17:29:29 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux. Error message

[root@hghosh yambo-master]# make all
for target in yambo ypp a2y p2y yambo_ph ypp_ph yambo_rt ypp_rt yambo_nl ypp_nl yambo_kerr ; do rm -f "/root/soft/yambo-master/bin/$target" ; make $target; if test ! -f "/root/soft/yambo-master/bin/$target" ; then echo "$target build failed"; break;fi ; done
make[1]: Entering directory `/root/soft/yambo-master'

>>>[Making libxc]
make[2]: Entering directory `/root/soft/yambo-master/lib/libxc'
( cd ../archive ; if ! test -e libxc-2.2.3.tar.gz ; then
cp Makefile.loc Makefile ; make libxc-2.2.3.tar.gz ; fi )
gunzip < ../archive/libxc-2.2.3.tar.gz | ../../config/missing --run tar xf -

gzip: stdin: unexpected end of file
tar: This does not look like a tar archive
tar: Exiting with failure status due to previous errors
gtar: This does not look like a tar archive
gtar: Exiting with failure status due to previous errors
WARNING: I can't seem to be able to run `tar' with the given arguments.
You may want to install GNU tar or Free paxutils, or check the
command line arguments.
make[2]: *** [uncompress-stamp] Error 1
make[2]: Leaving directory `/root/soft/yambo-master/lib/libxc'
make[1]: *** [ext-libs] Error 2
make[1]: Leaving directory `/root/soft/yambo-master'
yambo build failed

with many thanks and best regards
Soumyadeep

[andrea.ferretti]

this error usually means that the tar.gz archive is broken (failed download or similar situations).
Note that this can be due also to firewalls or other means of protecting compute clusters.

You can try to download the needed files yourself and place them in
yambo/lib/archive
urls are in yambo/lib/archive/package.list

hope it helps
Andrea

[soumyadeepghosh35]

The downloaded package in not broken because I installed it successfully in my Ubuntu PC. I think "firewalls or other means of protecting compute clusters" may be the possible cause.

thanks and best regards
Soumyadeep

[soumyadeepghosh35]

I have downloaded the packages (fftw-3.3.6-pl1.tar.gz; iotk-y1.2.2.tar.gz; libxc-2.2.3.tar.gz; netcdf-4.4.1.1.tar.gz) , place them at /lib/archive and get rid off previous problem. But this time face an new error,

Error: Assumed-shape array 'z4' at (1) cannot be an argument to the procedure 'c_loc' because it is not C interoperable
io_bulk.f90:352.26:

call C_F_POINTER(C_LOC(Z5), RZ5, isize_loc )
1
Error: Assumed-shape array 'z5' at (1) cannot be an argument to the procedure 'c_loc' because it is not C interoperable
make[2]: *** [io_bulk.o] Error 1
make[2]: Leaving directory `/root/soft/yambo-master/src/io'
make[1]: *** [yambo] Error 2
make[1]: Leaving directory `/root/soft/yambo-master'
yambo build failed

Please help.

with regards
Soumyadeep

[andrea.ferretti]

Dear Soumyadeep,

the fact that the error is now on io_bulk.F means that all external libraries have been properly compiled (or found) externally.
Now, the error on c_loc is usually related to old fortran/gcc. I think that if you switch to gcc 7 or newer the problem goes away.

take care
Andrea

[soumyadeepghosh35]

I have upgraded my gcc version to 7.3.0 but error still remains. I think yambo still configured with older gcc v4.8.5, check that

FC kind = gfortran GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)

Is it possible to configure with new gcc version.

with regards
Soumyadeep

[andrea.ferretti]

Dear Soumyadeep,

if you change compiler it is always a good idea to make a deep cleanup of the sources, issuing

Code: Select all

make distclean

Next, you need to re-configure and re-compile.
After the configuration, you should check which compiler is in use (should be gfortran and/or mpif90, I think) and again you need to check if you are
pointing to gcc v7 or v4 (eg gfortran -V).
If after the installation you are using v7 all good, just go ahead with the compilation.
If instead you have both versions installed, then you need to properly implement a switch from one to the other.
In this case you need to check gnu and ubuntu documentation. I did it for CentOS and I had to add the following lines
to my bashrc:

Code: Select all

source /opt/rh/devtoolset-7/enable

HTH
Andrea