Hi,
What is the output of
ldd /usr/local/software/amber16/bin/to_be_dispatched/antechamber
Hai
On Tue, Jan 23, 2018 at 10:06 PM Yuan Hu <Yuan.Hu.alkermes.com> wrote:
> Hi Scott,
>
> $/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).
>
> Best,
> Yuan
> Phone: 781-609-6975
> Office: 2A12-NW-A
>
>
> -----Original Message-----
> From: Scott Brozell [mailto:sbrozell.rci.rutgers.edu]
> Sent: Tuesday, January 23, 2018 7:13 PM
> To: AMBER Mailing List
> Subject: EXT: Re: [AMBER] Amber16 installation: Segmentation fault (core
> dumped) error when execute antechamber
>
> [EXTERNAL]
>
> Hi,
>
> 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)
> $AMBERHOME/bin/to_be_dispatched/antechamber "$."
> > >
> > >
> > > -Yuan
> > >
> > > Errors in the "make test" log file:
> > > make[2]: Entering directory
> `/usr/local/software/amber16/AmberTools/test/antechamber'
> >
> > ... removed - all show as above, ie: Segmentation fault
>
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Received on Tue Jan 23 2018 - 20:00:03 PST
