Re: [AMBER-Developers] compile errors

From: Jason Swails <>
Date: Thu, 25 Feb 2010 22:29:18 -0500

On Thu, Feb 25, 2010 at 10:04 PM, case <> wrote:
> On Thu, Feb 25, 2010, Jason Swails wrote:
>> A fresh checkout of Amber11 is giving the following errors when
>> compiled with intel compilers and intel MKL (linux em64t):
> Sigh...I am really looking forward to changing to git.  There have been
> something like 75 CVS commits today, so saying something like "a fresh
> checkout of Amber11" is only mildly helpful.  Once we make the change, you
> can specify an exact commit that I can be sure to reproduce.
>> 18:38:07 [linx64: ~] > ifort -V
>> Intel(R) Fortran Compiler for applications running on Intel(R) 64,
>> Version 10.1    Build 20080312 Package ID: l_fc_p_10.1.015
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>> 18:38:25 [linx64: ~] > icc -V
>> Intel(R) C Compiler for applications running on Intel(R) 64, Version
>> 10.1    Build 20080312 Package ID: l_cc_p_10.1.015
>> Copyright (C) 1985-2008 Intel Corporation.  All rights reserved.
>> 18:39:44 [linx64: ~] > echo $MKL_HOME
>> /opt/intel/mkl/
> Be sure you have again done "cvs co"; be sure you have re-configured; then
> post your config.h file (if the problem persists).  We particularly need to
> see what your FLIBS variable is.
>> /ufl/qtp/aer/gps/arwen_3/amber11/bin/nab -o matgen matgen.o
> Another idea: go to amber11/src/nss and type "nab -v matgen.o".  That will
> give verbose output that should help locate the problem.
>> /ufl/qtp/aer/gps/arwen_3/amber11/lib/libnab.a(pbsaapi.o)(.text+0x271):
>> In function `prepb_read_':
>> : undefined reference to `for_write_seq_lis'
> The entry point should be defined in libifcore.a in the library connected
> to your ifort compiler.  For me, this is in /opt/intel/fce/10.1.018/lib.
> So either your FLIBS variable doesn't have "-ifcore" in it, or it's in the
> wrong order, or the compiler is not looking in the proper directory, or....

Ugh. It's also possible that the group member that tried compiling
did not have their environment set (i.e. were not
sourced, and the intel compiler libraries were not in any library
path). I'll take a closer look at this, and we'll check out a *fresh*
copy tomorrow morning (whatever that may be :) ).

>> What's strange is that I did not get this error with the version 11
>> intel compilers (though this is a separate checkout by someone else in
>> our group, but it's new nonetheless).
> I don't see that there has been any change in the location of
> for_write_seq_lis between version 10 and 11 of ifort.  Also, things work for
> me for both verion 10.1.025 and 11.1.  So, I'm hoping that you just got
> trapped in an inconsitent CVS state.

He got the same errors in two *separate* checkouts today. I think his
environment may be more to blame. We subsequently tried with the gnu
compilers, since we figured it was a compiler issue and got an error
when compiling ptraj. I think it had something to do with declaring i
as an int in two for loops in the time correlation function. I took
"int" out of the for loops, but the compile still failed (I had lost
patience at this point and didn't pursue this much further... Also why
I didn't devote a post to it). Maybe it has something to do with a
possibly garbled CVS version that had already been torn through with
ifort as part of an incomplete environment setup. Who knows.
Tomorrow will bring new trials and hopefully brighter updates.

On a side note, I had only just learned about git a week or two ago as
one of Torvalds' *side* projects from (and for) the linux kernel. A
mildly impressive individual...


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Thu Feb 25 2010 - 19:30:04 PST
Custom Search