AMBER: xleap, opteron, pgi and segmentation fault.

From: Lars Packschies <>
Date: Wed, 26 Oct 2005 15:57:40 +0200

Dear Members,

  I have problems getting xleap to run. Amber8 (fully patched) is installed
on a dual opteron cluster in 64 bit using the PGI compilers 5.2-4 (serial
version). I applied the hints and tips on the PGI amber page
(<>). Everything
seems to run perfectly but xleap returns a segmentation fault.

  For any reason I cannot compile Amber (or leap...) in 32 bit mode. PGI
suggests to pactch the leap src Makefile (inserting X11LIBDIR after
"XHOME". I configured Amber with

  ./configure -nopar -opteron -acml -lapack pgf90

  and compiled with

  make -e YACC="/usr/bin/bison -y" X11LIBDIR="lib" serial

  In the end, it returns

/usr/bin/ld: skipping incompatible /usr/X11R6/lib/ when searching
for -lXt
/usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.a when searching
for -lXt
/usr/bin/ld: cannot find -lXt
make[2]: *** [xaLeap] Error 2
make[2]: Leaving directory `/home/a0580/amber/amber8/src/leap/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/a0580/amber/amber8/src/leap'
make: *** [serial] Error 2 is there (pointing to The cluster runs the Rocks
distribution (version 3 something).

  Long story short: Is there a way to compile Amber8 fully in 32 bit mode?
  As far as I understand, only leap is tried to be linked to the 32 bit
(Xt-)library, while all the other code is compiled natively in 64 bit. Or
do I really have a problem with an incompatible 32 bit X library?

  However, I'b be happy just with xleap runnung, all other binaries seem to
be fine.

  Do you have any suggestions?

  Thanks in advance,


             ,H  + Dr. Lars Packschies  ZAIK/RRZK, Robert-Koch-Str.10 +
H      H    O    | Chemistry Dpt. Support            D-50931 Cologne  |
 `O-H. |  ,' `H  | Comp.Dpt., Univ. of Cologne  Phn (+49)221-478-7022 |
      `O-H       +  Fax (+49)221-478-5568 +
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Received on Wed Oct 26 2005 - 15:53:00 PDT
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