> Have you tested this for side-effects? If not, how are you solving the
> problem at your site?
I've run all the tests with gfortran and pgf90 with my small changes to
files.h and do not see any errors related to that (but I do see others
as outlined below); (we were solving the problem currently by using
symbolic links or copying files around to directories with smaller paths).
p.s. DAC, I can get accounts for Ross and Mike if this will help with
pathscale access...
------------------
Other testing/compiling issues, snapshot 28mar:
** pentium, pgf90, -bintraj (configure -bintraj pgf90)
-- bintraj.f cannot find typesizes.mod (as a result of use netcdf)
solution: -I../netcdf/include added to AMBERFLAGS in config.h
[is this the best place for this? Maybe add to FFLAGS]
TESTS: all tests pass with -bintraj or files.h modifications
** opteron, gfortran, -bintraj (configure -bintraj gfortran)
-- mismatch with underscores between netcdf and amber
tried and did not work:
(1) remove -fno-second-underscore everywhere
(2) selectively add -fsecond-underscore
(3) change -Df2cfortrain to -DpgiFortran
solution: ? (idea's anyone???)
** opteron | pentium, pathscale, -bintraj
-- configure for netcdf fails; pathf90 does not produce an executable,
down the road you get messages like:
make[4]: Entering directory
`/uufs/inscc.utah.edu/common/home/cheatham/snapshot/icebox/pathscale-bintr
aj/amber9/src/netcdf/src/fortran'
pathcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O1 -I../libsrc
-DNDEBUG -DpgiFortran fort-attio.c
In file included from fort-attio.c:6:
ncfortran.h:27:42: NF_INT_IS_C_... not defined: No such file or
directory
Problem: Compiling the test program by the netcdf ./configure
fails due to the high optimization (foptflags) and then switches to
any other available compiler automagically (pgf90 in our case).
Replacing the foptflags by fflags fixes it.
Problem 2: No setting of NETCDF.mod
Problem 3: F/C linking, second underscore causes link failure
Problem 4: ptraj/rdparm: Need to define dependency for NETCDF.mod to
match netcdf.mod
SOLUTION: Modify f90ncflags/fncflags to be "fflags" rather than
"foptflags"
in configure, netcdf section
SOLUTION2: Add if bintraj netcdf=NETCDF.mod check in pathscale section
SOLUTION3: Add -fno-second-underscore to foptflags, fflags, cflags in
pathscale section of configure.
SOLUTION4: Add NETCDF.mod:: dependency like netcdf.mod
** opteron | pentium, pathscale (-bintraj or no -bintraj)
-- lot's of warnings in ameoba compiling:
pathf90-1542 pathf90: WARNING XFORM_MPOLE_MATRIX, File =
_amoeba_multipoles.f, Line = 851, Column = 8
Initializing a named common block member in a program unit other than a
block data is not legal for this architecture.
data hind4 /1,2,3,2,3,1,3,1,2,2,3,3,3,3,2/
^
** opteron, pathscale
-- internal compiler error on force.PIMD
dropping optimization to -O2 allows it to continue.
** opteron, gfortran (no -bintraj)
-- compiles fine, but test error with ./Run.noesy
[I do not know how to fix this]
From noesy.out:
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 03/30/2006 at 12:26:55
[-O]verwriting output
File Assignments:
| MDIN: mdin
| MDOUT: noesy.out
|INPCRD: 01.ann10.xyz
| PARM: prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
just get final values
&cntrl
ntx=1, ntb=0,
pencut= 0.1, nmropt=2, ipnlty=1,
imin=1, maxcyc=1,
ntc=1, ntf=1, cut=9.0,
mxsub=10, tausw=0.101,
/
&wt type='NOESY', istep1=0,istep2=500,value1=1.0,
value2=1.0, /
&wt type='END' /
NOESY=NXP.8May95
DISANG=RST.16sept93
LISTOUT=POUT
...
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
NOESY 0 500 1.000000 1.000000 0 0
RESTRAINTS:
Requested file redirections:
NOESY = NXP.8May95
DISANG = RST.16sept93
LISTOUT = POUT
Restraints will be read from file: RST.16sept93
Here are comments from the DISANG input file:
#
# 1 GUA h1p 1 GUA h2d 2.7 (#141
Number of restraints read = 590
Done reading weight changes/NMR restraints
Noesy volumes will be read from file: NXP.8May95
Here are comments from the NOEsy input file:
# first pass at fixed-distance file
#
Namelist reports error in reading noeexp
-- Subscript out of range implies dimensioning problem
-- (see nmr.h)
Received on Wed Apr 05 2006 - 23:49:33 PDT
