[xcrysden] Running XCrySDen

[Gavin Abo]

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 <xcrysden-bounces at democritos.it> 
> en nombre de Gavin Abo <gabo13279 at gmail.com>
> *Enviado:* miércoles, 28 de agosto de 2024 08:16 p. m.
> *Para:* xcrysden at democritos.it <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/
>     <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/
>     <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>
>           o 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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