Hi,
1.
What is different between your two workstations?
(Run ldd on the workstation that works and compare to below.)
On Wed, Jan 24, 2018 at 01:19:13PM +0000, Yuan Hu wrote:
> $ldd /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> linux-vdso.so.1 => (0x00007ffcba57b000)
> libesets_pac.so => /usr/lib64/libesets_pac.so (0x00007f268172e000)
> libm.so.6 => /usr/lib64/libm.so.6 (0x00007f268142c000)
> libc.so.6 => /usr/lib64/libc.so.6 (0x00007f2681069000)
> libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f2680e4d000)
> libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f2680c48000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f268188a000)
2.
On the broken workstation a debug version of antechamber,
run it, and send the output including the stack trace:
cd AmberTools/src/antechamber/
make clean
make install AMBERBUILDFLAGS='-g -O0'
ls -l /usr/local/software/amber16/bin/to_be_dispatched/antechamber
/usr/local/software/amber16/bin/to_be_dispatched/antechamber
scott
On Wed, Jan 24, 2018 at 03:06:11AM +0000, Yuan Hu wrote:
>
> $/usr/local/software/amber16/bin/to_be_dispatched/antechamber
> Segmentation fault (core dumped)
>
> Another workstation is also Red Hat Enterprise Linux Server release 7.2 (Maipo).
>
> -----Original Message-----
> From: Scott Brozell [mailto:sbrozell.rci.rutgers.edu]
>
> Ok, but what is the result of running on your original workstation this command:
> /usr/local/software/amber16/bin/to_be_dispatched/antechamber
>
> The result on your other workstation is the expected result.
> what is the OS on your other workstation ?
>
> scott
>
> On Tue, Jan 23, 2018 at 09:27:41PM +0000, Yuan Hu wrote:
> > I think that may be some library file got overwritten by other programs. I tried to reinstall amber16, but it didn't solve the problem.
> > I copied the compiled antechamber executable in "../to_be_dispatched/antechamber" to another workstation which doesn't have amber installed. It can print out welcome message.
> >
> > $./antechamber
> >
> > Welcome to antechamber 17.3: molecular input file processor.
> >
> > ./antechamber: Fatal Error!
> > AMBERHOME is not set.
> >
> > -----Original Message-----
> > From: Scott Brozell [mailto:sbrozell.rci.rutgers.edu]
> > Sent: Tuesday, January 23, 2018 3:12 PM
> > To: AMBER Mailing List
> > Cc: Yuan Hu
> > Subject: EXT: Re: [AMBER] Amber16 installation: Segmentation fault
> > (core dumped) error when execute antechamber
> >
> > Why do you think anaconda3 is the problem ?
> >
> > PLease enter this command:
> > /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> >
> > If it seg faults then it is clear that the problem is antechamber (or some antechamber specific OS preamble).
> >
> > I do not have problems with:
> > gcc version 4.8.5 (GCC)
> > Red Hat Enterprise Linux Server release 6.9 (Santiago)
> >
> > scott
> >
> > On Tue, Jan 23, 2018, Yuan Hu wrote:
> > > I'm trying to install Amber16 with AmberTools17 with the following command.
> > > ./configure --python-install local --with-python /usr/bin/python2.7
> > > gnu My workstation is using Red Hat Enterprise Linux Server release 7.2 (Maipo).
> >
> > On Tue, Jan 23, 2018 at 06:41:28AM +0000, Yuan Hu wrote:
> > >
> > > Thanks for the reply. I will answer your questions in line.
> > > I think there may be some interfering with anaconda3. Please see more details in question 4.
> > >
> > > 1. What is the result of typing "gcc --version"?
> > >
> > > gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
> > >
> > > 2. Do programs not from the antechamber directory work OK? What
> > > happens if you type "make test" in the $AMBERHOME directory? [You
> > > can hit control-C if all the tests appear to be failing...no need to
> > > wait for thousands of error messages....; on the other hand, it
> > > might be that non-antehcamber tests generally pass, and that would
> > > be good information to know.]
> > >
> > > Yes, other programs work fine. I went through all the programs in the $AMBERHOME/bin, all the failed programs are from antechamber directory. Interestingly, several tools in that folder are fine, such as bondtype, database, espgen, match, parmcal.
> > > Here is the "make test" result, the errors in the log file are attached to the end.
> > >
> > > make[1]: Leaving directory `/usr/local/software/amber16/AmberTools/test'
> > > 1993 file comparisons passed
> > > 18 file comparisons failed
> > > 16 tests experienced errors
> > > Test log file saved as
> > > /usr/local/software/amber16/logs/test_at_serial/2018-01-22_23-56-27.
> > > lo
> > > g
> > > No test diffs to save!
> > >
> > > 3. Did you source the $AMBERHOME/amber.sh file in the terminal session that is failing?
> > >
> > > Yes. I sourced $AMBERHOME/amber.sh
> > >
> > > 4. Do you have older versions of amber on your machine that might somehow be interfering?
> > >
> > > I don't have older versions of AMBER on the machine, but I found the same antechamber and other AmberTool programs in /usr/local/software/anaconda3/bin/. The anaconda3 was installed after I built AMBER.
> > > Something I want to mention, I installed AMBER16 first, and did a quick test of antechamber. it works fine right after the installation. Then I installed anaconda3 to install openmm, pdbfixer, lomap and yank. After those installations, I tested antechamber again, and fount it broken.
> > > I tried to remove anacoda3 from my $PATH, $LD_LIBRARY_PATH, $PYTHONPATH, but got no luck to make antechamber work.
> > > $echo $PATH
> > > /usr/local/software/amber16/bin::/usr/local/bin:/usr/bin:/usr/local/
> > > sb in:/usr/sbin:/usr/local/cuda-8.0/bin
> > >
> > > $echo $LD_LIBRARY_PATH
> > > /usr/local/software/amber16/lib:/usr/lib64:/usr/lib:/usr/local/lib:/
> > > li
> > > b:/usr/local/cuda-8.0/lib64/:/usr/lib64/openmpi/lib:/usr/local/cuda/
> > > li
> > > b64
> > >
> > > $echo $PYTHONPATH
> > > /usr/lib64/python2.7/site-packages:/usr/lib/python2.7/site-packages:
> > > /u sr/local/software/amber16/lib/python2.7/site-packages
> > >
> > > $antechamber
> > > /usr/local/software/amber16/bin/antechamber: line 4: 7113 Segmentation fault (core dumped) $AMBERHOME/bin/to_be_dispatched/antechamber "$."
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Received on Thu Jan 25 2018 - 11:00:04 PST
