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
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Thu May 30 2019 - 07:30:03 PDT
