From minkyupark.phys at gmail.com Thu Apr 4 07:09:24 2024 From: minkyupark.phys at gmail.com (=?utf-8?B?67CV66+86rec?=) Date: Thu, 4 Apr 2024 14:09:24 +0900 Subject: [xcrysden] Compile on M2 Message-ID: <340FFBBB-0CC3-4B84-AC9D-D20AA1DC9CC2@gmail.com> Dear all, I have been trying to compile xcrysden on M2 chip without success. I found one relevant email http://www.democritos.it/pipermail/xcrysden/2022-September/002116.html But this does not work for me. While ago, I was able to compile xcrysden on MacBook Pro with intel chip by installing required libraries through homebrew. But even if I follow the same procedure, it does not work in M2. So does anyone succeed to compile xcrysden on M2 or any other apple silicon chips? Attaches are my Make.sys and output error message. Best, Minkyu Park Korea Research Institute of Standards and Science ?? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: err.log Type: application/octet-stream Size: 33553 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment-0001.obj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment-0002.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Make.sys.txt Url: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment-0001.txt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20240404/77eab2ad/attachment-0003.htm From bogus@does.not.exist.com Thu Apr 4 08:40:47 2024 From: bogus@does.not.exist.com () Date: Thu, 04 Apr 2024 06:40:47 -0000 Subject: No subject Message-ID: 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=3D/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directoryEN_TOPDIR=3D/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directory ------------------------------ In the xcrysden page it says; * * Linux x86_64 binary packages (64bit): * Shared: xcrysden-1.6.2-linux_x86_64-shared.tar.gz * Requires: libtk8.6.so, libtcl8.6.so, libTogl.so.2, libGLU.so.1, li= bGL.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 lib= fftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5 =DAltima comprobaci=F3n de caducidad de metadatos hecha hace 2:37:04, el mi= =E9 28 ago 2024 13:17:04. No se encontraron coincidencias. (=3D>there were no coincidences) Saludos Pablo --_000_BY5PR06MB667609773C2282D58C4EB11ACB962BY5PR06MB6676namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I found it;
----
# find / -name *libtk8.6*
/opt/intel/oneapi/intelpython/python3.9/pkgs/tk-8.6.10-hbc83047_0/lib/libtk= 8.6.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: mi=E9rcoles, 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 e= rror "libtk8.6.so: cannot open shared object file: No such file or dir= ectory".


From the message, it look= s like XCrySDen cannot find the libtk8.6.so file.


That file should be in yo= ur /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 like= ly 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=3D/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directoryEN_TOPDIR=3D/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directory
------------------------------
In the xcrysden page it says;

  • Linux x86_64 binary packages (64bit):
    • -------------------------
    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 lib= fftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5
    =DAltima comprobaci=F3n de caducidad de metadatos hecha hace 2:37:04, el mi= =E9 28 ago 2024 13:17:04.
    No se encontraron coincidencias.
    (=3D>there were no coincidences)

    Saludos

    Pablo
    --_000_BY5PR06MB667609773C2282D58C4EB11ACB962BY5PR06MB6676namp_-- From bogus@does.not.exist.com Thu Apr 4 08:40:47 2024 From: bogus@does.not.exist.com () Date: Thu, 04 Apr 2024 06:40:47 -0000 Subject: No subject Message-ID: 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=3D/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directoryEN_TOPDIR=3D/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directory ------------------------------ In the xcrysden page it says; * * Linux x86_64 binary packages (64bit): * Shared: xcrysden-1.6.2-linux_x86_64-shared.tar.gz * Requires: libtk8.6.so, libtcl8.6.so, libTogl.so.2, libGLU.so.1, li= bGL.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 lib= fftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5 =DAltima comprobaci=F3n de caducidad de metadatos hecha hace 2:37:04, el mi= =E9 28 ago 2024 13:17:04. No se encontraron coincidencias. (=3D>there were no coincidences) Saludos Pablo --_000_BY5PR06MB66767AF7E697D1219D8603AACB972BY5PR06MB6676namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
    Estimado Gavin,

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

    ./ftnunit: error while loading shared libraries: libgfortran.so.5: cannot o= pen 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<= /div>
    /opt/intel/oneapi/intelpython/python3.9/pkgs/_openmp_mutex-4.5-1_gnu/info/r= ecipe/parent/install-libgfortran.sh
    /opt/intel/oneapi/intelpython/python3.9/pkgs/libgcc-ng-9.3.0-h5101ec6_17/in= fo/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/f40/286405d7= 78e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfo= rtran.so.5
    /var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d7= 78e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfo= rtran.so.5.0.0

    how to link intel fortran with xcrysden

    Pablo
    De: xcrysden-bounces at democr= itos.it <xcrysden-bounces at democritos.it> en nombre de Gavin Abo <g= abo13279 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 m= ight explain why you would need the libtk8.6.so from the operating system package that was compiled with GCC for being abl= e 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/l= ibtk8.6.so (instead of /lib64/libtk8.6.so), it is likely that you would nee= d to compile XCrySDen using xcrysden-1.6.2.tar.gz and you would need to mod= ify 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-de= vel package. The tk-devel package when installed puts libtk.so (i.e., libtk= 8.6.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/libtk= 8.6.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: x= crysden-bounces at democritos.it <xcrysden-bounces at democritos.it> en nombre de Gavin Abo &l= t;gabo13279 at gmail.com>
    Enviado: mi=E9rcoles, 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 erro= r "libtk8.6.so: cannot open shared object file: No such file or direct= ory".


    From the message, it looks l= ike XCrySDen cannot find the libtk8.6.so file.


    That file should be in your = /lib64 directory:


    username at fedora:~$ ls -l /li= b64/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=3D/home/Programas/xcrysden-1.6.2-bin-shared
    XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp

    /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directoryEN_TOPDIR=3D/home/Programas/xcrysden-1.6.2-bin-shared
    XCRYSDEN_SCRATCH=3D/home/pablo/xcrys_tmp

    /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading sh= ared libraries: libtk8.6.so: cannot open shared object file: No such file o= r directory
    ------------------------------
    In the xcrysden page it says;

  • Linux x86_64 binary packages (64bit):
    • -------------------------
    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 lib= fftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5
    =DAltima comprobaci=F3n de caducidad de metadatos hecha hace 2:37:04, el mi= =E9 28 ago 2024 13:17:04.
    No se encontraron coincidencias.
    (=3D>there were no coincidences)

    Saludos

    Pablo
    --_000_BY5PR06MB66767AF7E697D1219D8603AACB972BY5PR06MB6676namp_--