[xcrysden] Running XCrySDen

[Gavin Abo]

I tried it out.  It seems to work as seen in the screenshot at:


https://github.com/gsabo/xcrysden-Patches/blob/main/Fedora%2040%20XCrySDen%201.6.2.png


Apparently, Fedora 40 ships with gcc version 14:


username at fedora:~$ gfortran --version
GNU Fortran (GCC) 14.2.1 20240801 (Red Hat 14.2.1-1)
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Most of the Fedora 34 steps still applied to Fedora 40, but I had to 
make some adjustments in order to get it to work as follows.


Since you already have Fedora 40 installed, you can skip to step 8 below.


1. Went to: https://getfedora.org/en/workstation/download/
2. Downloaded Fedora Workstation 40:
Fedora-Workstation-Live-x86_64-40-1.14.iso
3. Downloaded Fedora Media Writer Windows:
FedoraMediaWriter-win32-latest.exe
4. Ran: FedoraMediaWriter-win32-latest.exe
    a. Clicked "I Agree"
    b. Clicked "Install"
    c. Clicked "Next"
    d. With "Run Fedora Media Writer" selected, clicked "Finish"
    e. Selected "Select .iso file", then clicked "Next"
    f. Clicked "Select..."
    g. Selected "Fedora-Workstation-Live-x86_64-40-1.14.iso", then 
clicked "Open"
    h. Selected USB Drive, then clicked "Write"
    i. Click "Finish"
    j. Closed the Fedora Media Write dialog (upper right x in window)
5. Booted from the USB stick
6. Installed Fedora 40
     a. Selected "Start Fedora-Workstation-Live 40"
     b. Clicked "Install Fedora..."
     c. Selected English and clicked Continue
     d. Clicked "Installation Destination"
     e. Clicked Done
     WARNING: The steps f-h will wipe everything for starting fresh with 
the drive.
     f. Clicked "Reclaim space"
     g. Clicked "Delete all"
     h. Clicked "Reclaim space"
     i. Clicked "Begin Installation"
     j. Clicked "Finish Installation"
     k. In Fedora Live, click on bar with power icon, click on power 
icon, click "Restart", click "Restart" button
7. Setup Fedora 40
     a. Clicked "Start Setup"
     b. Click Skip (or setup Wi-Fi)
     c. Turn off "Location Services" and "Automatic Problem Reporting", 
then click Next
     d. Click "Enable Third-Party Repositories", then click Next
     e. Type a Full Name and Username and click Next
     f. Type a password and click Next
     g. Click "Start Using Fedora Linux"
     h. For tour prompt, click "Skip"
8. Opened a terminal in Fedora 40 and performed the following:

username at fedora:~$ sudo yum install patch ImageMagick openbabel 
mesa-libGL-devel mesa-libGLU-devel tcl-devel tk-devel fftw-devel 
libXmu-devel gfortran
...
Is this ok [y/N]: y
...
username at fedora:~$ wget 
https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-src.tar.gz/download
...
username at fedora:~$ tar xvf download
...
username at fedora:~$ cd Togl2.0/
username at fedora:~/Togl2.0$  ./configure --with-tcl=/usr/lib64 
--with-tk=/usr/lib64 --enable-64bit
...


The Togl 2.0 failed due the gcc version 14 compiler as seen here:


username at fedora:~/Togl2.0$ make
gcc -DPACKAGE_NAME=\"Togl\" -DPACKAGE_TARNAME=\"togl\" 
-DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"Togl\ 2.0\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 
-DHAVE_SYS_PARAM_H=1 -DUSE_THREAD_ALLOC=1 -D_REENTRANT=1 
-D_THREAD_SAFE=1 -DTCL_THREADS=1 -DMODULE_SCOPE=extern\ 
__attribute__\(\(__visibility__\(\"hidden\"\)\)\) 
-D_LARGEFILE64_SOURCE=1 -DTCL_WIDE_INT_IS_LONG=1 -DUSE_TCL_STUBS=1 
-DUSE_TK_STUBS=1 -DAUTOSTEREOD=\"\" -I"/usr/include/tcl-private/generic" 
-I"/usr/include/tcl-private/unix" -I"/usr/include/tk-private/generic" 
-I"/usr/include/tk-private/unix" 
-I"/usr/include/tk-private/generic/ttk"     -pipe -m64 -O2 
-fomit-frame-pointer -Wall -Wno-implicit-int -fPIC  -c `echo togl.c` -o 
togl.o
togl.c: In function ‘Togl_Init’:
togl.c:928:26: error: assignment to ‘void (*)(struct Tk_Window_ *, 
Tk_ClassProcs *, void *)’ from incompatible pointer type ‘void 
(*)(struct Tk_Window_ *, const Tk_ClassProcs *, void *)’ 
[-Wincompatible-pointer-types]
   928 |         SetClassProcsPtr = tkStubsPtr->tk_SetClassProcs;
       |                          ^
make: *** [Makefile:357: togl.o] Error 1


However, I was able to patch it for continuing with the build:


username at fedora:~/Togl2.0$ wget 
https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/togl.patch

username at fedora:~/Togl2.0$ patch -b togl.c togl.patch
username at fedora:~/Togl2.0$ make

...

username at fedora:~/Togl2.0$ cd ..
username at fedora:~$ wget 
http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz
...
username at fedora:~$ tar xvf xcrysden-1.6.2.tar.gz
...
username at fedora:~$ cd xcrysden-1.6.2/
username at fedora:~/xcrysden-1.6.2$ cp system/Make.sys-semishared Make.sys
username at fedora:~/xcrysden-1.6.2$ wget 
https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Make-fedora34.patch
...
username at fedora:~/xcrysden-1.6.2$ patch -b Make.sys Make-fedora34.patch
patching file Make.sys
username at fedora:~/xcrysden-1.6.2$ make all
...

Note: username in commands below should be replaced with your user name.

username at fedora:~/xcrysden-1.6.2$ echo 'export 
XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$ echo 'export 
PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$ echo 'export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$ source ~/.bashrc


Best Regards,

Gavin

XCrySDen user


On 8/26/2024 10:56 PM, delamora wrote:
> Dear Gavin,
> Thank for your reply, I will try it.
> Yes, I have the Fedora 40
> Pablo
> ------------------------------------------------------------------------
> The issue might be because the version of Fedora that you are using 
> does not have the operating system library that it needs to load 
> ftnunit.  Thus, the "error while loading" error.
>
>
> What is the Fedora version?  The xcrysden-1.5.60-bin-semishared worked 
> with around Fedora versions 25 to 27.
>
>
> With Fedora 34, xcrysden 1.6.2 was used, but it had to be compiled.
>
>
> The compile steps used were given the post at:
>
>
> http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html 
> <http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html>
>
>
> At https://fedoraproject.org <https://fedoraproject.org> , I see that 
> Fedora is now at version 40.  I've not tried XCrySDen 1.6.2 with that 
> version if that is what you are using.
>
>
> With some other code packages, I have seen some GNU compiler 
> compatibility issues encountered with newer Linux distributions that 
> release with gcc/g++ version 13.  With Ubuntu 24.04 LTS that comes 
> with gcc/g++ version 13, though, I was able to fall back as a 
> workaround (while waiting to see if the code developers would provide 
> new versions with code changes for working with the newer compilers) 
> for example by installing a g++ version 10 package using "sudo apt 
> install g++-10".  Don't know yet if there are any issues compiling 
> XCrySDen 1.6.2 with the latest gcc versions or if Fedora has a similar 
> fall back package that can be installed like Ubuntu.
>
>
> Kind Regards,
>
> Gavin
>
> XCrySDen user
>
>
> On 8/26/2024 2:24 PM, delamora wrote:
>
>     I have Fedora Linux
>     I installed xcrysden-1.5.60-bin-semishared, but when I try to open it
>     "xcrysden"
>     it does not open, it gives the error;
>
>     /home/Programas/xcrysden-1.5.60-bin-semishared/bin/ftnunit: error
>     while loading
>
>     How can I fix it
>
>     Yours
>
>     Pablo
>
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