Re: amber-developers: pgf90 and netcdf

From: Scott Brozell <>
Date: Fri, 31 Mar 2006 22:19:13 -0700


exe/README does not contain all the executables.

Several tests are hanging.
The fix is to turn down the optimization of src/lapack/dlamch.f
I changed line 42 of src/lapack/Makefile to
   $(FC) -c -o $. _$<
and rdc and noesy below ran ok.
I'll rebuild and retest everything later.


ps details

./configure -bintraj pgf90
pgf90 6.0-8 32-bit target on x86 Linux
Linux piv-login1 2.4.24-pre1 #6 SMP Wed May 19 09:47:10 EDT 2004 i686 i686
i386 GNU/Linux
GNU gdb Red Hat Linux (

1. cd rdc; ./Run.dip
I tried to use gdb but it is seg faulting on the where command after
complaining that the stack frame is corrupted:
#1 0x08482a2d in dlamc1_ ()
#2 0x08482ae0 in dlamc2_ ()
#3 0x08482349 in dlamch_ ()
#4 0x08492b36 in dspev_ ()
#5 0x08637402 in .C1_351 ()
#6 0x00000001 in ?? ()
#7 0x00000001 in ?? ()
#8 0xbfffc418 in ?? ()
#9 0x0858b635 in f90io_fmtw_end ()

Totalview shows:
     dlamc3_, FP=bfffcc60
     dlamc1_, FP=bfffcc60
     dlamc2_, FP=bfffccb0
     dlamch_, FP=bfffcce0
     dspev_, FP=bfffced0
     align1, FP=bfffced0
     force, FP=bfffd078
     runmin, FP=bfffd340
     sander, FP=bfffd700
     multisander, FP=bfffd710
     main, FP=bfffd740
     __libc_start_main, FP=bfffd768

on line 519 of align.f.

Here is the tail of mdout:
 Requested file redirections:
  DISANG = RST.allang
  DIPOLE = RST.dip
 Restraints will be read from file: RST.allang
Here are comments from the DISANG input file:
# 1 GUA H1' 1 GUA H3' 4.6

                       Number of restraints read = 793

                  Done reading weight changes/NMR restraints

 Alignment info will be read from file: RST.dip
 Here are comments from the alignment input file:

 Number of triangulated 3-point waters found: 0

2. cd tgtmd/change_target; ./Run.tgtmd
3. cd tgtmd/change_target.rms; ./Run.tgtmd
4. cd tgtmd/conserve_ene; ./Run.tgtmd
5. cd tgtmd/minimize; ./Run.tgtmin
6. cd tgtmd/PME; ./Run.tgtPME
7. cd trajene; ./Run.trajene
8. cd noesy; ./Run.noesy
9. cd neb_gb; ./
Received on Wed Apr 05 2006 - 23:49:31 PDT
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