AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler

From: Jiten <>
Date: Sun, 11 Jul 2004 00:30:15 +0900

Dear All,

I am trying install amber8 in Opteron processor with Linux. I have PGI-workstation version as the compiler. First of all I fix all the bugs available in amber home for amber8.


1. ./configure -opteron -big -verbose pgf90

2. make serial > log

I found that most of the modules have been compiled except the Xaleap becuase of X11 problem, with the following error.

PGC-W-0118-Function XAPESetTorsionLabel does not contain a return statement (xaParmEditor.c: 582)
PGC-W-0118-Function XAPESetImproperLabel does not contain a return statement (xaParmEditor.c: 597)
PGC-W-0118-Function XAPESetHBondLabel does not contain a return statement (xaParmEditor.c: 613)
PGC/x86-64 Linux/x86-64 5.1-6: compilation completed with warnings
/usr/bin/ld: skipping incompatible /usr/X11R6/lib/ when searching for -lXt
/usr/bin/ld: cannot find -lXt
make[2]: *** [xaLeap] Error 2
make[1]: *** [install] Error 2
make: *** [serial] Error 2

I have the following few questions.

1. How can I fix this problem ; any suggestion

2. I try to test run by using : make -i test

cd dmp; ./Run.dmp
  ./Run.dmp: Program error
make: [test.sander.no_lmod] Error 1 (ignored)
cd adenine; ./Run.adenine
  ./Run.adenine: Program error
make: [test.sander.no_lmod] Error 1 (ignored)
cd cytosine; ./Run.cytosine
  ./Run.cytosine: Program error
make: [test.sander.no_lmod] Error 1 (ignored)
cd nonper; ./Run.nonper
  ./Run.nonper: Program error
make: [test.sander.no_lmod] Error 1 (ignored)

It seems to me that even the amber8 modules have not been compiled properly. ( In my previous experience with amber7 shows that even if xaLeap was not compiled properly, other amber7 modules work fine)
I attach the log file  ( from :  make serial > log )for the reference.
I would highly appreciate for your kind suggestions.
N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399) 
Web : and
Home Page :

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Received on Sat Jul 10 2004 - 16:53:00 PDT
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