RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem

From: Shekter, Lee <>
Date: Wed, 23 Mar 2005 11:29:57 -0500

Hello -
Well, a colleague in my IT department suggest a fix for my most recent compile problem. The error message was this:
/usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.a when searching for -lXt
/usr/bin/ld: cannot find -lXt

The fix was this:

Line 114 of $AMBERHOME/src/leap/src/leap/Makefile changed to "lib64" from "lib" in order for AMBER to compile against the 64-bit version of the Xt libraries

Now, AMBER8 compiles completely, using ./configure -p4 -static -ifort, yet when I cd'd to the test directory and issued a "make test" command, I got this:

cd dmp; ./Run.dmp
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander 0821AF57 Unknown Unknown Unknown
sander 08075636 Unknown Unknown Unknown
sander 08048268 Unknown Unknown Unknown
sander 08289FA0 Unknown Unknown Unknown
sander 08048121 Unknown Unknown Unknown
  ./Run.dmp: Program error
make: *** [test.sander.no_lmod] Error 1

The last line is similar to previously reported errors, usually caused by not sourcing (I *do* source it, and if I issue an echo $LD_LIBRARY_PATH I get this: /opt/intel/mkl72/lib/32:/opt/intel_fc_81/lib), but the SIGSEGV? This error was also reported on Aug 6, 2004 but in that user's case, all the tests had run successfully. I can't run any.

I am using the most recent Intel Fortran, Version 8.1, Build 20050207, Package ID: l_fc_pc_8.1.024 along with gcc 3.2.3 on a dual Xeon EM64T machine with RHEL 3.0, update 4.

Lee Shekter

Assistant Professor (Adjunct) Medical Science
Brown University
Divison of Biology and Medicine
Box G
Providence, RI 02912-9107
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Received on Wed Mar 23 2005 - 16:53:00 PST
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