Thank you for the explanation. I was able to successfully compile Amber (using miniconda) after renaming the miniconda ld.
It would be a good idea to have this information added to the installation page (
http://ambermd.org/Installation.php) or maybe even the manual.
Best,
Mohtadin
-----Original Message-----
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, May 30, 2019 1:23 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] compiling Amber Tools 19
Non-UNMC email
hi, this is a known issue with Anaconda python in some Linux distro.
The issue here is that Anaconda provides its own `ld` program that's not compatitble with your system.
can you please try to rename
"/opt/amber19/amber18/miniconda/compiler_compat/ld" to "/opt/amber19/amber18/miniconda/compiler_compat/ld-old" to force to use system `ld` program? Then "make install" again.
Related:
-
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pytorch_pytorch_issues_16683-23issuecomment-2D459982988&d=DwIGaQ&c=ZukO2fIan9e5E9v43wuy1w&r=AK606AZl4zLFP6DQFHRjBg0DSGYp515YmJqZ3zuhSTk&m=MxDWQS6oPdywzH6nQ03IYFKZcg18EeQyGMbJ_6ydlVw&s=JiP5Zja9TbCZind0x2U5fQJCWPpTRmxsd5cHdA7Zu-g&e=
- google search
<
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.google.com_search-3Fei-3DwRzwXImBGYWp-5FQaN1YvgBQ-26q-3Dminiconda-2Bunable-2Bto-2Binitialize-2Bdecompress-2Bstatus-2Bfor-2Bsection-2B.debug-5Finfo-26oq-3Dminiconda-2Bunable-2Bto-2Binitialize-2Bdecompress-2Bstatus-2Bfor-2Bsection-2B.debug-5Finfo-26gs-5Fl-3Dpsy-2Dab.3...84340.85138..85554...0.0..0.276.1030.1j1j3......0....1..gws-2Dwiz.-5FmHh8RYRQnE&d=DwIGaQ&c=ZukO2fIan9e5E9v43wuy1w&r=AK606AZl4zLFP6DQFHRjBg0DSGYp515YmJqZ3zuhSTk&m=MxDWQS6oPdywzH6nQ03IYFKZcg18EeQyGMbJ_6ydlVw&s=6QsOfM_e-OSxhRVLCYvX15cT2XU8PMVIt7SJ4EGbck0&e= >
Hai
On Thu, May 30, 2019 at 10:00 AM Hashemi, Mohtadin < mohtadin.hashemi.unmc.edu> wrote:
> I have a very similar issue during configure of AmberTools19, but my
> issue during make is with parmed. I did not troubleshoot for very long
> since it was in a production environment, but a similar failure also
> happens on my personal computer. My system is Arch Linux (fully
> updated as of Tuesday) using GCC 8.3.0. Amber18 and AmberTools18
> compile and run normally on the same system; I did compilation from
> scratch earlier this morning to see if something was wrong with the host system.
>
> These are the steps for configure and make:
> ./configure -noX11 gnu
> source amber.sh
> make
>
> Attached are the stdout during configure, stderr during configure, and
> output during make.
>
> The relevant section of the make output:
>
> make[2]: Entering directory '/opt/amber19/amber18/AmberTools/src'
> (cd parmed &&
> PYTHONPATH=/opt/amber19/amber18/lib/python2.7/site-packages
> /opt/amber19/amber18/bin/amber.python setup.py install -f
> --prefix=/opt/amber19/amber18 > build.log)
> warning: no files found matching 'versioneer.py'
> cc1plus: warning: command line option '-Wstrict-prototypes' is valid
> for C/ObjC but not for C++
> cc1plus: warning: command line option '-Wstrict-prototypes' is valid
> for C/ObjC but not for C++
> src/readparm.cpp: In function 'ExitStatus readparm(const string&,
> std::vector<std::__cxx11::basic_string<char> >&, ParmDataMap&,
> ParmStringMap&, ParmStringMap&, ParmFormatMap&, std::__cxx11::string&)':
> src/readparm.cpp:143:28: warning: 'char* strncpy(char*, const char*,
> size_t)' specified bound 8 equals destination size [-Wstringop-truncation]
> strncpy(d.c, word.c_str(), MAX_HOLLERITH_SIZE);
> ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /opt/amber19/amber18/miniconda/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/src/_rdparm.o: unable to initialize
> decompress status for section .debug_info
> /opt/amber19/amber18/miniconda/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/src/_rdparm.o: unable to initialize
> decompress status for section .debug_info
> /opt/amber19/amber18/miniconda/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/src/_rdparm.o: unable to initialize
> decompress status for section .debug_info
> /opt/amber19/amber18/miniconda/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/src/_rdparm.o: unable to initialize
> decompress status for section .debug_info
> build/temp.linux-x86_64-2.7/src/_rdparm.o: file not recognized: file
> format not recognized
> collect2: error: ld returned 1 exit status
> error: command 'g++' failed with exit status 1
> make[2]: *** [Makefile:525: parmed] Error 1
> make[2]: Leaving directory '/opt/amber19/amber18/AmberTools/src'
> make[1]: *** [Makefile:56: serial] Error 2
> make[1]: Leaving directory '/opt/amber19/amber18/AmberTools/src'
> make: *** [Makefile:7: install] Error 2
>
>
> Using the system Python (both 2.7 and 3.7) during
> configure/compilation I am able to successfully compile a working AmberTools19/Amber18 suite.
> However, it is not a viable solution because the production
> environment does not allow change to the python installation.
>
> Best,
> Mohtadin
>
>
> -----Original Message-----
> From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
> Date: Tue, 28 May 2019 14:37:07 +0200
>
> Sorry for not being completely clear ...
>
> Basically I just did a simple "./configure gnu" from $AMBERHOME and
> said "Yes" when configure was asking me whether to download and
> install miniconda ....
>
> See attached the output of "$AMBERHOME/AmberTools/src/configure_python "
>
> It does look to me like some python packages get compiled at this
> stage and the error pops up during these compilations (e.g. line 1299
> in the attached file) ...
>
> This may or may not be different between Tools 18 and 19. I forgot I
> performed an OS update before compiling Tools 19 (did not try to
> recompile
> 18 after this update) ... So, the error might have something to do
> with that OS update ... And of course, with software that is not under
> your control ...
>
> But maybe this thread helps to track this down or at least to point
> people with the solution with using the system's python just in case
> anybody gets similar issues ...
>
> Vlad
>
>
> On 5/28/19 1:38 PM, David A Case wrote:
> > On Tue, May 28, 2019, Vlad Cojocaru wrote:
> >> The first time I got the error was during the first configure step
> >> (serial compilation). The error appears when building package
> >> subprocess32 during the compilation of miniconda (I run configure
> >> with minicoda compilation). Parts of the error are below.
> > Can you say exactly what arguments you gave to the configure script?
> > Did you say "yes" to downloading miniconda? As far as I know, there
> > is nothing that is supposed to be compiled at that step, and I've
> > never seen an error like this before. It doesn't sound like anything
> > that changed between AmberTools18 and AmberTools19.
> >
> > As you found out, you can use the --with-python flag: it can point
> > to your system python, or to the minconda python that was downloaded
> > in your AmberTools18 install. That way, you will have all the needed
> > modules.
> >
> > [Aside: I'm not sure whether everything in Amber actually works with
> > Python 3.7, althought the things you are most likely to use are.]
> >
> > If you wish, can you post the entire output of running
> > AMBERHOME/AmberTools/src/configure_python (this is what the
> > configure script is running)? This seems like a miniconda
> > problem--still our problem, since we ask users to rely on that--but
> > one that involves third party codes that we don't control.
> >
> > ...thanks....dac
> >
> >
> > _______________________________________________
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> >
>
> --
> Vlad Cojocaru, PD (Habil.), Ph.D.
> -----------------------------------------------
> Project Group Leader
> Department of Cell and Developmental Biology Max Planck Institute for
> Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany
> -----------------------------------------------
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Thu May 30 2019 - 12:30:02 PDT
