[xcrysden] Running XCrySDen

[delamora]

Estimado Gavin,

Running xcrysden, now it opens, but it gives this error;

./ftnunit: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory

I have intel fortran in

pablo at fedora:/home/Programas/xcrysden-1.6.2-bin-shared$ locate libgfortran
/opt/intel/oneapi/intelpython/python3.9/pkgs/_openmp_mutex-4.5-1_gnu/info/recipe/parent/install-libgfortran.sh
/opt/intel/oneapi/intelpython/python3.9/pkgs/libgcc-ng-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh
/opt/intel/oneapi/intelpython/python3.9/pkgs/libgomp-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh
/opt/intel/oneapi/intelpython/python3.9/pkgs/libstdcxx-ng-9.3.0-hd4cf53a_17/info/recipe/parent/install-libgfortran.sh
/var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5
/var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5.0.0

how to link intel fortran with xcrysden

Pablo
________________________________
De: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> en nombre de Gavin Abo <gabo13279 at gmail.com>
Enviado: jueves, 29 de agosto de 2024 09:50 p. m.
Para: xcrysden at democritos.it <xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen


XCrySDen 1.6.2 works with Fedora 40 when libtk8.6.so from the operating system tk-devel package is used.


I've not tried libtk8.6.so from Intel's OneAPI.  That library file likely was compiled with the Intel compiler. So, it might be that the file has different function declarations than that produced by GCC.  That might explain why you would need the libtk8.6.so from the operating system package that was compiled with GCC for being able to use xcrysden-1.6.2-linux_x86_64-shared.tar.gz.


Thus, if you wanted to use /opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so (instead of /lib64/libtk8.6.so), it is likely that you would need to compile XCrySDen using xcrysden-1.6.2.tar.gz and you would need to modify Make.sys yourself to use the OneAPI compiler.  Since that is probably a more difficult approach, I would recommend using the operating system version of libtk8.6.so instead.


For that, at [1], the webpage shows the Fedora 40 operating system tk-devel package. The tk-devel package when installed puts libtk.so (i.e., libtk8.6.so) also in the directory:


/usr/lib64/


With Fedora 40, when I checked that directory, the libtk8.6.so was there:


username at fedora:~$ ls -l /usr/lib64/libtk*
-rwxr-xr-x. 1 root root 1343528 Jan 26  2024 /usr/lib64/libtk8.6.so
lrwxrwxrwx. 1 root root      11 Jan 26  2024 /usr/lib64/libtk.so -> libtk8.6.so
-rwxr-xr-x. 1 root root    6640 Jan 26  2024 /usr/lib64/libtkstub8.6.a


When the tk-devel package has been successfully installed, the terminal should show the same or similar terminal display of:


username at fedora:~$ sudo yum install tk-devel
[sudo] password for username:
Last metadata expiration check: 0:27:44 ago on Thu 29 Aug 2024 09:16:34 PM MDT.
Package tk-devel-1:8.6.13-3.fc40.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!


[1] https://packages.fedoraproject.org/pkgs/tk/tk-devel/fedora-40.html


Kind Regards,

Gavin

XCrySDen user


On 8/29/2024 10:37 AM, delamora wrote:
I found it;
----
# find / -name *libtk8.6*
/opt/intel/oneapi/intelpython/python3.9/pkgs/tk-8.6.10-hbc83047_0/lib/libtk8.6.so
/opt/intel/oneapi/intelpython/python3.9/envs/2022.0.2/lib/libtk8.6.so
/opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so
----
but xcrysden does not find it

Pablo
________________________________
De: xcrysden-bounces at democritos.it<mailto:xcrysden-bounces at democritos.it> <xcrysden-bounces at democritos.it><mailto:xcrysden-bounces at democritos.it> en nombre de Gavin Abo <gabo13279 at gmail.com><mailto:gabo13279 at gmail.com>
Enviado: miércoles, 28 de agosto de 2024 08:16 p. m.
Para: xcrysden at democritos.it<mailto:xcrysden at democritos.it> <xcrysden at democritos.it><mailto:xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen


I see that you have the error "libtk8.6.so: cannot open shared object file: No such file or directory".