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

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 20 Oct 2015 20:55:59 -0400

On Tue, Oct 20, 2015 at 8:07 PM, case <dacase.scarletmail.rutgers.edu>
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
>
> Oooh...it 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?) 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 libsander.so).

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.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 20 2015 - 18:00:03 PDT
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