Hi Joao,
I haven't used the tarball from the webpage in a while, but you should use
the update_amber wrapper (section 2.4.2 in the Amber23 manual). Check the
options there with --help. If starting from AmberTools 22 code, you should
run --update and / --upgrade. Your .patches folder should get populated
then.
Best regards,
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
---------------------------------------------------------------------------------------------
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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El lun, 21 ago 2023 a las 11:03, Damas Joao CHST (<Joao.Damas.syngenta.com>)
escribió:
> Hi Stephan, sorry for the late reply.
>
>
>
> Thanks for the clarification about the Amber/AmberTools versioning
> interplay, that helps clarify things. I’ll just trust the download page
> then and ignore the numbers in the source.
>
>
>
> I did not apply any pytraj patches and the .patches folders are all empty
> in the installation. Is there something I’m missing from my installation
> procedure?
>
>
>
> Yes, I know I could just apply the patch you gave me (thanks for it, it
> works!), but I like to do “from scratch” installations often, to validate
> my processes, and it allowed me to identify these issues I stated. I’ll
> need to change my installation from using miniconda, due to Anaconda ToS.
> Is what is found on point 3 of section 2.2.5 of the manual the full
> instructions? Are there any version constraints?
>
>
>
> Thanks,
>
> João
>
>
>
> *From:* Stephan Schott <s.schott-verdugo.fz-juelich.de>
> *Sent:* Wednesday, August 9, 2023 1:14 PM
> *To:* Damas Joao CHST <Joao.Damas.syngenta.com>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] questions about AmberTools installation from source
>
>
>
> *CAUTION:* This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe.
>
>
> ------------------------------
>
> Hi again Joao,
>
>
>
> The 22/23 version number has to do with the fact that Amber as a whole has
> a new version released every 2 years, while AmberTools is released yearly.
> Because of that, you will find many 22 pointers throughout the code. That
> said, many codes that were updated for AmberTools23 might have forgotten to
> change the release date, but overall the last AmberTools is still tailored
> for Amber22.
>
>
>
> I am not sure about the pytraj errors you are seeing, but they *might* be
> related to a recent patch that was passed to update pytaj and make it
> python 3.11 / Cython compatible. Did you apply the last pytraj patch? You
> should have the update.3 file under ".patches/AmberTools23_Applied_Patches"
> if that is the case.
>
>
>
> P.S., if the trigger was the packmol-memgen numpy floats, the patch is
> still not there; you don't need to recompile, if you changed the calls as I
> mentioned before.
>
>
>
> Best regards,
>
>
>
> Stephan Schott Verdugo
>
> Biochemist
>
>
>
> Computational Biophysical Chemistry
>
> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
>
> Forschungszentrum Jülich GmbH
>
> Wilhelm-Johnen-Straße, 52425 Jülich
> Germany
>
>
>
>
> ------------------------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
> Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
>
> ------------------------------------------------------------------------------------------------
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> ------------------------------------------------------------------------------------------------
>
>
>
>
>
> El mié, 9 ago 2023 a las 10:41, Damas Joao CHST via AMBER (<
> amber.ambermd.org>) escribió:
>
> Dear all,
>
> Triggered by a patching on my installation due to a bug found, I was
> looking a bit deeper in some details, and I have a few questions.
>
> I am installing AmberTools from source (option 3). This is mainly because
> I'm doing a cluster-wide installation for multiple users and since we use
> environment modules, we found that this is the best approach. Up to here,
> all good.
>
> My first question is: I got the current source through the website,
> compared the md5sum, all checks out. I was expecting to have version 23,
> but when I look at the source, several places (e.g., CMakeLists.txt)
> mention that it is version 22. I wonder if this is just a bug (i.e., it's
> version 23 but the version strings were not updated) or if it's a source of
> AmberTools 22.
>
> My second question: when patching, I like to do an installation from
> scratch, applying the suggested patch after. When I was recompiling, the
> process errored, while it did not in the past. I paste here a few of the
> lines of the output, even if there are many more similar errors:
>
> pytraj/topology/topology.cpp: In function '__pyx_CoroutineObject*
> __Pyx__Coroutine_NewInit(__pyx_CoroutineObject*, __pyx_coroutine_body_t,
> PyObject*, PyObject*, PyObject*, PyObject*, PyObject*)':
> pytraj/topology/topology.cpp:47943:23: error: '_PyErr_StackItem' {aka
> 'struct _err_stackitem'} has no member named 'exc_type'
> 47943 | gen->gi_exc_state.exc_type = NULL;
> | ^~~~~~~~
> pytraj/topology/topology.cpp:47945:23: error: '_PyErr_StackItem' {aka
> 'struct _err_stackitem'} has no member named 'exc_traceback'
> 47945 | gen->gi_exc_state.exc_traceback = NULL;
> | ^~~~~~~~~~~~~
> pytraj/topology/topology.cpp: At global scope:
> pytraj/topology/topology.cpp:48152:1: error: too many initializers for
> 'PyTypeObject' {aka '_typeobject'}
> 48152 | };
> | ^
> error: command '/progs/all/opensource/gcc/11.3.0/bin/gcc' failed with exit
> code 1
> make[2]: ***
> [AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Error 1
> make[1]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Error 2
> make: *** [all] Error 2
>
> My first guess was python version incompatibility, since I think before
> the miniconda being installed was with python 3.10, and now it was
> installing 3.11 (since the default in cmake is "latest" and I guess the
> latest has changed since the last time I installed). I added
> "-DMINICONDA_VERSION=py310_23.5.2-0" to my cmake flags, and all compiled
> fine. Do you have cross-compilation matrix for several version of python?
> It would be good to know which versions AmberTools is compatible with since
> the only reference in the manual is that it needs to be Python 3.4 or
> greater.
>
> On the same note, looking at the cmake scripts, I noticed AmberTools is
> getting the installer from Anaconda/Continuum. Due to Anaconda's ToS, I'll
> need to change that (follow point 3 of section 2.2.5 of the manual) and it
> would be good to know which versions of python are possible to use.
> Additionally, are the python packages references in the manual (numpy,
> scipy, matplotlib, cython, setuptools, and tkinter) the only ones needed?
> Any specific versions or the latest should work?
>
> Thank you for your time,
> João
>
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> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr.
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Received on Mon Aug 21 2023 - 03:30:02 PDT
