amber-developers: pathscale, gfortran and pgf90 problems

From: David A. Case <>
Date: Fri, 31 Mar 2006 09:14:43 -0700

On Fri, Mar 31, 2006, Thomas E. Cheatham, III wrote:
> p.s. DAC, I can get accounts for Ross and Mike if this will help with
> pathscale access...

Please do that. How about one for me?

In general, you should try out pmemd as well (with the -bintraj option).
Bob ostensibly has this stuff working for pathf90 and pgf90 compilers.
Maybe that will provide a clue as to what you should do with sander/ptraj.

> ** pentium, pgf90, -bintraj (configure -bintraj pgf90)
> -- bintraj.f cannot find typesizes.mod

We need to find the cause of this problem. Is pgf90 naming its mod files
something different? What is the name of the netcdf mod file? Is there
a "netcdf.mod" file in src/sander when bintraj is being compiled? Is
there a NETCDF.mod file? The latter is trivial to fix: see how sgi_mips
is handled.

> ** 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

John may be able to help here. But again, some details would help. What
is an example of a mismatch? I never understood why the configure has
-DPGIFortran anyway. Which version of gcc are you using?

> ** 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
-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

How about using gcc instead of pathcc?

> Problem 2: No setting of NETCDF.mod

See the "netcdf" and "netcdflib" variables in configure. Can't you do the
same thing that is done for sgi_mips? (That compiler also creates
rather than netcdf.mod.)

> SOLUTION4: Add NETCDF.mod:: dependency like netcdf.mod

Where?? This is already done in src/sander/Makefile. It looks like it is
needed in src/ptraj/Makefile.

> ** opteron | pentium, pathscale (-bintraj or no -bintraj)
> 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/
> ^

We get these on SGI as well, be they seem to not be fatal. The other Tom
even less time than you do, so it's going to have to be a fatal error to
any attention from him.

> ** opteron, gfortran (no -bintraj)
> -- compiles fine, but test error with ./Run.noesy
> [I do not know how to fix this]

Same problem as with absoft: it apparently cannot read 2-dimensional
in a namelist, or the required syntax is different that I expect. Someone
could play with this, but I am frankly amazed that gfortran works at

Can I assume you will be sending me patches?


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Wed Apr 05 2006 - 23:49:32 PDT
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