Re: [AMBER-Developers] AmberTools configure failure and compilation errors

From: case <>
Date: Sun, 11 Apr 2010 09:51:16 -0400

On Sun, Apr 11, 2010, Sally Pias wrote:

> ==========
> A configure failure using intel 10 compilers:
> ==========
> $ arch
> x86_64
> $ source /opt/intel/fc/10.1.015/bin/
> $ source /opt/intel/cc/10.1.015/bin/

I think you have to subsitute "fce" for "fc (and "ice" for "ic") in the above

> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> ld: skipping incompatible /usr/lib/ when searching for -lm
> ./configure: line 854: ./testp: No such file or directory
> Error: Unable to compile a C program using icc -D_FILE_OFFSET_BITS=64
> Please check your compiler settings or configure flags.

Configure is correct here: you compiler is not set up correctly. We generally
ask users who report this problem to use the Google bar at the Amber web site.
For example, searching for "skipping incompatible" will get you the right
info. I don't think that trying to have configure understand all possible
errors is the way to go.

> ==========
> A serial compilation error with GNU compilers on the same system
> (using ./configure -static -noX11 gnu):

> _safemem.f: In function 'reallocate_pointer_1d_character':
> _safemem.f:914: internal compiler error: Segmentation fault

Looks like this is gcc 4.1.x. What is the value of "x", and which Linux?
There are lots of problems with 4.1.2 (still widely distributed, thanks
to RedHat,Fedora,CentOS) but we haven't seen a compilation failure before.

> A similar serial compilation error with GNU compilers on a different
> system (using ./configure -static -noX11 gnu):

???? Looks like the same compiler error.

> ==========
> A parallel compilation error using Intel 11.1 compilers (using
> ./configure -static -noX11 -mpi intel):

> $ export PATH=/opt/mpich2-1.0.7/bin:$PATH

(Be sure that this mpich2 was compiled with the same compilers you are using
for amber. Also, I'm getting some weird errors with -static and openmpi with
the intel compilers. But neither of these seem relevant to your problem.)

> ar: creating libsff.a
> make[2]: write error

Out of disk space? Failing hard drive? It's not clear what the underlying
problem is, but it looks like something not under our control.

...thanks for the reports...dac

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Received on Sun Apr 11 2010 - 07:00:03 PDT
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