Re: [AMBER-Developers] Second release candidate for AmberTools 1.3

From: Volodymyr Babin <vbabin.ncsu.edu>
Date: Thu, 24 Sep 2009 23:44:06 -0400 (EDT)

> The configure file now supports the Portland group compilers...I hope
> someone
> will try this out (we don't have these installed here.)

We have some old (6.0) version around and it goes as follows:

1. netcdf/src/config.guess could not guess the LIBC for CC=pgcc

diff -u amber11.old/src/netcdf/src/config.guess
amber11/src/netcdf/src/config.guess
--- amber11.old/src/netcdf/src/config.guess 2008-04-15 19:23:12.000000000
-0400
+++ amber11/src/netcdf/src/config.guess 2009-09-24 22:39:49.671624833 -0400
.. -153,7 +153,7 ..
         LIBC=gnu
         #endif
 EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep LIBC= | sed -e 's: ::g'`
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep LIBC | sed -e 's: ::g'`
 fi

 # Note: order is significant - the case branches are not exclusive.

----------------

2. cpp -traditional -P -DNO_SANDER_DIVCON -DBINTRAJ sqm.f > _sqm.f
pgf90 -c -O1 -Mfree -o sqm.o _sqm.f
PGF90-S-0038-Symbol, command_argument_count, has not been explicitly
declared (_sqm.f)
  0 inform, 0 warnings, 1 severes, 0 fatal for sqm

tried 'iargc()' -- same result [cutting edge fortran?]

-----------------

3. commented out the 'sqm' target in the toplevel Makefile

-----------------

4. PGC-S-0032-Syntax error: Unexpected input at '/' (./ptraj_local.h: 79)
PGC-S-0029-Syntax error: Recovery attempted by deleting from '/' on line
79 through identifier trajs on line 79 (./ptraj_local.h)

C++ style comment in line 79

-----------------

5. PGC-S-0035-Syntax error: Recovery attempted by replacing '/' by double
0.00000000000000000E+0 (rdparm.c: 710)

-----------------

6. few more C++ comments in the io.c, trajectory.c, ptraj.c

-----------------

7. C++ comment in leap/src/leap/[unit.c,tools.c]

-----------------

8. gleap

 pgCC -c -I../../freelib -I../../freelib -o numvec.o numvec.cpp
"numvec.hpp", line 27: warning: omission of explicit type is nonstandard
          ("int" assumed)
          template< typename T > numvec( const std::_Expr<T,double>& rhs )
: std::valarray<double>( rhs ) {}

>> commented it out in Makefile_at

-----------------

9. nab

pgcc -c -Dflex -O2 -DBINTRAJ -o nmode.o nmode.c
PGC-S-0040-Illegal use of symbol, _Complex
(/usr/include/bits/cmathcalls.h: 54)
PGC-W-0114-More than one type specified (/usr/include/bits/cmathcalls.h: 54)
PGC-S-0029-Syntax error: Recovery attempted by deleting from identifier
__z on line 54 to just before ')' on line 54
(/usr/include/bits/cmathcalls.h: 54)
PGC-S-0040-Illegal use of symbol, _Complex
(/usr/include/bits/cmathcalls.h: 54)
PGC-W-0114-More than one type specified (/usr/include/bits/cmathcalls.h: 54)
...

>> commented out in Makefile_at

============================================================================

relevant tests PASSED ok

============================================================================

./configure -oldmkl -mpi pgi

went ok, but

make -f Makefile_at parallel

stopped quickly with

mpicc -c -Dflex -O2 -DBINTRAJ -DMPI -o nmode.o nmode.c
PGC-S-0040-Illegal use of symbol, _Complex
(/usr/include/bits/cmathcalls.h: 54)
PGC-W-0114-More than one type specified (/usr/include/bits/cmathcalls.h: 54)
...

---------------------

cd ptraj; make parallel :

utility.o(.text+0xac6): In function `netcdfDefineDimension':
: undefined reference to `nc_def_dim'

(many more)

compiled OK with libnetcdf.a added by hands.

Best,

Volodymyr


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Received on Thu Sep 24 2009 - 21:00:02 PDT
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