[xcrysden] Running XCrySDen
delamora
delamora at unam.mx
Wed Sep 4 19:23:53 CEST 2024
Dear Gavin,
This is the error that I got running xcrysden;
---------------
Error in startup script: Can not set ident to a window path name
Couldn't configure togl widget
while executing
------------------
just installed
tcl-togl
tcl-togl-devel
opengl
Saludos
Pablo
________________________________
De: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> en nombre de delamora <delamora at unam.mx>
Enviado: lunes, 2 de septiembre de 2024 11:02 a. m.
Para: XCrySDen mailing list <xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen
Dear Gavin,
I try to install what is suggested in the xcrysden page;
----------------------------------------------------------
dnf install tk libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick openbabel libgfortran5
Última comprobación de caducidad de metadatos hecha hace 0:05:30, el lun 02 sep 2024 09:38:00.
El paquete tk-1:8.6.13-3.fc40.x86_64 ya está instalado.
No hay coincidencias para el argumento: libglu1-mesa
No hay coincidencias para el argumento: libtogl2
No hay coincidencias para el argumento: libfftw3-3
No hay coincidencias para el argumento: libxmu6
No hay coincidencias para el argumento: imagemagick
* Tal vez quiso decir: ImageMagick
No hay coincidencias para el argumento: libgfortran5
Error: No se pudo encontrar ningún resultado: libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick libgfortran5
-----------------------------------
There were no results for
libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick libgfortran5
but
ImageMagick
is already installed.
Cheers
Pablo
________________________________
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".
From the message, it looks like XCrySDen cannot find the libtk8.6.so file.
That file should be in your /lib64 directory:
username at fedora:~$ ls -l /lib64/libtk8.6.so
-rwxr-xr-x. 1 root root 1343528 Jan 26 2024 /lib64/libtk8.6.so
If it isn't, the package for it might not be installed.
In Fedora 40, it was likely installed by the command:
sudo yum install tk-devel
Kind Regards,
Gavin
XCrySDen user
On 8/28/2024 4:59 PM, delamora wrote:
I got the
xcrysden-1.6.2-bin-shared
then I ran
xcrysden
and I got
-------------
[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
Code available from http://www.xcrysden.org/.
XCRYSD[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
Code available from http://www.xcrysden.org/.
XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp
/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.6.so: cannot open shared object file: No such file or directoryEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp
/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.6.so: cannot open shared object file: No such file or directory
------------------------------
In the xcrysden page it says;
*
* Linux x86_64 binary packages (64bit):
* Shared: xcrysden-1.6.2-linux_x86_64-shared.tar.gz<http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz>
* Requires: libtk8.6.so, libtcl8.6.so, libTogl.so.2, libGLU.so.1, libGL.so.1, libfftw3.so.3, libXmu.so.6, libX11.so.6, libgfortran.so.5, ..
-------------------------
so I searched for these packages and I got
dnf search libtk8.6.so libtcl8.6.so libTogl.so.2 libGLU.so.1 libGL.so.1 libfftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5
Última comprobación de caducidad de metadatos hecha hace 2:37:04, el mié 28 ago 2024 13:17:04.
No se encontraron coincidencias.
(=>there were no coincidences)
Saludos
Pablo
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