Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber

From: Scott Brozell <>
Date: Tue, 23 Jan 2018 15:12:14 -0500


Why do you think anaconda3 is the problem ?

PLease enter this command:

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)


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 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.log
> No test diffs to save!
> 3. Did you source the $AMBERHOME/ file in the terminal session that is failing?
> Yes. I sourced $AMBERHOME/
> 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/sbin:/usr/sbin:/usr/local/cuda-8.0/bin
> /usr/local/software/amber16/lib:/usr/lib64:/usr/lib:/usr/local/lib:/lib:/usr/local/cuda-8.0/lib64/:/usr/lib64/openmpi/lib:/usr/local/cuda/lib64
> /usr/lib64/python2.7/site-packages:/usr/lib/python2.7/site-packages:/usr/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 - 12:30:03 PST
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