AMBER Archive (2008)

Subject: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7

From: Atro Tossavainen (
Date: Wed Feb 13 2008 - 07:31:54 CST

I'm using

./configure -opteron pgf90

on's Murska cluster. I have applied today's bugfix.all which
includes everything up to bugfix.64. Everything is fine up until

pgcc -o makeDIST_RST makeDIST_RST.o -lm
/usr/bin/ld: warning: i386 architecture of input file `makeDIST_RST.o' is incompatible with i386:x86-64 output
makeDIST_RST.o(.text+0xe3d): In function `correct_upperbound':
: undefined reference to `__mth_i_dlogx'
makeDIST_RST.o(.text+0xe4a): In function `correct_upperbound':
: undefined reference to `__mth_i_dexpx'
make[2]: *** [makeDIST_RST] Error 2
make[2]: Leaving directory `/home/u3/tossavai/amber8/src/nmr_aux/prepare_input'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/u3/tossavai/amber8/src/nmr_aux'
make: *** [serial] Error 2

which goes away if the "-tp k8-32" flag is included manually:

~/amber8/src % cd nmr_aux/prepare_input
~/amber8/src/nmr_aux/prepare_input % pgcc -tp k8-32 -o makeDIST_RST makeDIST_RST.o -lm
~/amber8/src/nmr_aux/prepare_input %

Afterwards, I go back to $AMBERHOME/src, make serial again, and the
previous step deletes my hand-built binary, so I lose... :-)

Adding $(CFLAGS) to the Makefile in nmr_aux/prepare_input, after $(LOADCC)
and before -o makeWHATEVER, makes this go away. I wonder if it breaks
stuff on other platforms?

This also happens in src/leap/src/leap with

pgcc -o utilMakeHelp basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o utilMakeHelp.o -lm

and the same fix makes it go away.

Next, I'm trying to "make test", but sander segfaults... Where do I
start trying to figure this out?

Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
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