Re: [AMBER-Developers] Problems with AmberTools 15 and netcdf-fortran-4.2 compile

From: Ross Walker <>
Date: Tue, 20 Oct 2015 19:08:37 -0700

> On Oct 20, 2015, at 17:55, Jason Swails <> wrote:
> On Tue, Oct 20, 2015 at 8:07 PM, case <>
> wrote:
>> On Tue, Oct 20, 2015, Ross Walker wrote:
>>> I am trying to get an AWS AMI of AMBER up and running. This involves
>>> using Amazon's hacked up version of Linux which is loosely based on
>>> Redhat but has then been 'tweaked' in tons of ways. Anyway, long story
>>> short AmberTools 15 configure is dying:
>>> /usr/bin/ld:
>> /usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a(reshape_i4.o):
>> relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making
>> a shared object; recompile with -fPIC
>>> /usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a: could not read
>> symbols: Bad value
>> doesn't like libgfortran.a! Seems hard for us to fix.
>> Can you play around with things like "yum install netcdf" (or netcdf-devel,
>> etc.)? Then use the --with-netcdf flag to point configure to that.
> ‚ÄčI'm with Dave here. The problem seems to be that PIC is really not
> supported by gfortran on that platform. It's the first Linux I've seen of
> its kind (any chance of convincing Amazon to start supporting PIC in their
> platform?)

Ha ha ha ha... ROFLMAO... Convince Amazon??? That's the funniest thing I ever heard. ;-)

> I don't know that simply yum installing netcdf is going to work
> -- it'll get past the configure stage, but it may promptly choke on linking
> any executable (at the very least, it will choke on any of the shared
> objects that it tries to build, like

There isn't a netcdf package available in the yum repository they provide so I can't 'easily' yum install on it - I could download a Redhat RPM and try it but I think that would be hacky and unlikely to work. It is a weird weird weird Linux... They have Redhat AMI's which I could use - and already did successfully (without the GPU support) only to find out that only the Amazon Linux images support spot pricing (which is like 10% of on demand pricing) so other os's are not really a viable option.

> Another thing to try -- do a global delete of "-fPIC" in configure2 and try
> that. That will prevent the sander API, MDGX API, pysander, and pytraj
> codes from working on that platform. But if that doesn't matter, the rest
> of AmberTools should still work.

Yeah I tried this already but it didn't seem to work - at least making sure it doesn't get passed to the netcdf configure doesn't help - the auto config still detects support for -fPIC in the compiler and tries to use it - I need to look more closely at the various arguments that can be passed to configure. I think the issue is that some of the system libraries clearly somehow weren't compiled with -fPIC. I might be able to hack through some more and see if I can really remove everything.

The other option 'maybe' would be to try a completely different compiler suite. Any idea if that would work? - I could also try forcing on an older copy of devtools or manually replacing the suspect library since I have root access to the image. Any ideas on the best place to start?

The odd thing is that netcdf-4.3.0 seems to compile fine, it is just the netcdf-fortan-4.2 that fails. How hard would it be to switch to netcdf-4.3.0 for everything?

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Oct 20 2015 - 19:30:03 PDT
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