From mille121 at illinois.edu  Fri Dec 18 16:30:27 2009
From: mille121 at illinois.edu (Phil Miller)
Date: Fri, 18 Dec 2009 16:30:27 -0600
Subject: [charm] MPI 6.1.3 build error on NCSA AC cluster
In-Reply-To: <Pine.LNX.4.63.0912181606170.25236@lisboa.ks.uiuc.edu>
References: <Pine.LNX.4.63.0912181606170.25236@lisboa.ks.uiuc.edu>
Message-ID: <81f018ac0912181430m2c727470h8c30e1942cf7e45c@mail.gmail.com>

On Fri, Dec 18, 2009 at 16:17, Jim Phillips <jim at ks.uiuc.edu> wrote:
> Hi,
>
> I get this error building mpi-linux-x86_64-mpicxx on NCSA's AC cluster.
>
> [jphillip at ac ~]$ which mpicxx
> /usr/mvapich2-intel/bin/mpicxx
> [jphillip at ac ~]$ which icc
> /opt/intel/Compiler/11.1/038/bin/intel64/icc
>
> Any ideas or workaround? ?I've never seen this before. ?Looks like a yacc
> conflict with mvapich2, but charmxi doesn't need to be built with mpicxx.

Try changing CMK_NATIVE_{CC,CXX,LD,LDXX} from the respective CMK_FOO
variables to the underlying icc/icpc in
src/arch/mpi-linux-x86_64/conv-mach-mpicxx.sh.

Phil

> -Jim
>
>
> ../bin/charmc -host ?-language c++ -cp ../bin/ -o charmxi xi-main.o
> xi-symbol.o
> xi-grammar.tab.o xi-scan.o xi-util.o sdag-globals.o CSdagConstruct.o
> CEntry.o
> /usr/mvapich2-intel/lib/libmpich.a(parser.o):(.bss+0x18): multiple
> definition of
> ?`yyin'
> xi-scan.o:(.bss+0x38): first defined here
> /usr/mvapich2-intel/lib/libmpich.a(parser.o):(.bss+0x20): multiple
> definition of
> ?`yyout'
> xi-scan.o:(.bss+0x40): first defined here
> ld: Warning: alignment 8 of symbol `yylval' in xi-grammar.tab.o is smaller
> than
> 32 in /usr/mvapich2-intel/lib/libmpich.a(tokens.o)
> Fatal Error by charmc in directory
> /usr/tmp/charm_release-2.7b2.mpi-linux-x86_64
> -mpicxx/charm-6.1.3/mpi-linux-x86_64-mpicxx/tmp
> ? Command mpicxx -o charmxi xi-main.o xi-symbol.o xi-grammar.tab.o xi-scan.o
> xi
> -util.o sdag-globals.o CSdagConstruct.o CEntry.o -L../bin/../lib returned
> error
> code 1
> charmc exiting...
> gmake[1]: Leaving directory
> `/var/tmp/charm_release-2.7b2.mpi-linux-x86_64-mpicx
> x/charm-6.1.3/mpi-linux-x86_64-mpicxx/tmp'
> gmake[1]: *** [../bin/charmxi] Error 1
> gmake: *** [headers] Error 2
> -------------------------------------------------
> Charm++ NOT BUILT. Either cd into mpi-linux-x86_64-mpicxx/tmp and try
>
>


From mille121 at illinois.edu  Fri Dec 18 16:39:13 2009
From: mille121 at illinois.edu (Phil Miller)
Date: Fri, 18 Dec 2009 16:39:13 -0600
Subject: [charm] Charm 6.1.3 Release
Message-ID: <81f018ac0912181439t3bdc971cndc37da7a9fc39860@mail.gmail.com>

Charm stable version 6.1.3 has been released, with the following changes:
    * Updated to revised network and CPU Topology API
    * Fixed memory leaks on Infiniband Verbs layer.
    * Fix failure of quiescense detection in the presence of immediate messages.
    * Eliminated path conflicts between native MPI and AMPI.
    * Fix some bugs in configuration scripts.
    * Improve availability of memory-usage statistics
    * Platform-specific fixes on:
          o Generic MPI builds
          o Updated for newer versions of Microsoft compilers and
libraries, and build with Microsoft's MPI
          o Build and run script fixes on BlueGene machines.
          o Updated for newer versions of Portland Group (PGI) compiler.
          o Support newer releases of Mac OS X

http://charm.cs.uiuc.edu/download/downloads.shtml

Known Issues:
Recent versions of IBM's xlC compiler suite expose alignment/padding
issues in the runtime code, leading to application crashes. If you
encounter problems after moving to a new compiler, please check the
download page for an update or contact us at charm at cs.illinois.edu for
a patch. This is fixed in the development tree of Charm, which will
eventually be released as Charm 6.2.

From jim at ks.uiuc.edu  Fri Dec 18 17:13:27 2009
From: jim at ks.uiuc.edu (Jim Phillips)
Date: Fri, 18 Dec 2009 17:13:27 -0600 (CST)
Subject: [charm] MPI 6.1.3 build error on NCSA AC cluster
In-Reply-To: <81f018ac0912181430m2c727470h8c30e1942cf7e45c@mail.gmail.com>
References: <Pine.LNX.4.63.0912181606170.25236@lisboa.ks.uiuc.edu>
	<81f018ac0912181430m2c727470h8c30e1942cf7e45c@mail.gmail.com>
Message-ID: <Pine.LNX.4.63.0912181706440.25236@lisboa.ks.uiuc.edu>


It's easier to just switch mpiCC to mpicxx in 
src/arch/mpi-linux-x86_64/conv-mach.sh, since that file does the right 
thing by using gcc for the native compiles.

I can just define the MPICXX environment variable instead, right?

-Jim


On Fri, 18 Dec 2009, Phil Miller wrote:

> On Fri, Dec 18, 2009 at 16:17, Jim Phillips <jim at ks.uiuc.edu> wrote:
>> Hi,
>>
>> I get this error building mpi-linux-x86_64-mpicxx on NCSA's AC cluster.
>>
>> [jphillip at ac ~]$ which mpicxx
>> /usr/mvapich2-intel/bin/mpicxx
>> [jphillip at ac ~]$ which icc
>> /opt/intel/Compiler/11.1/038/bin/intel64/icc
>>
>> Any ideas or workaround? ?I've never seen this before. ?Looks like a yacc
>> conflict with mvapich2, but charmxi doesn't need to be built with mpicxx.
>
> Try changing CMK_NATIVE_{CC,CXX,LD,LDXX} from the respective CMK_FOO
> variables to the underlying icc/icpc in
> src/arch/mpi-linux-x86_64/conv-mach-mpicxx.sh.
>
> Phil
>
>> -Jim
>>
>>
>> ../bin/charmc -host ?-language c++ -cp ../bin/ -o charmxi xi-main.o
>> xi-symbol.o
>> xi-grammar.tab.o xi-scan.o xi-util.o sdag-globals.o CSdagConstruct.o
>> CEntry.o
>> /usr/mvapich2-intel/lib/libmpich.a(parser.o):(.bss+0x18): multiple
>> definition of
>> ?`yyin'
>> xi-scan.o:(.bss+0x38): first defined here
>> /usr/mvapich2-intel/lib/libmpich.a(parser.o):(.bss+0x20): multiple
>> definition of
>> ?`yyout'
>> xi-scan.o:(.bss+0x40): first defined here
>> ld: Warning: alignment 8 of symbol `yylval' in xi-grammar.tab.o is smaller
>> than
>> 32 in /usr/mvapich2-intel/lib/libmpich.a(tokens.o)
>> Fatal Error by charmc in directory
>> /usr/tmp/charm_release-2.7b2.mpi-linux-x86_64
>> -mpicxx/charm-6.1.3/mpi-linux-x86_64-mpicxx/tmp
>> ? Command mpicxx -o charmxi xi-main.o xi-symbol.o xi-grammar.tab.o xi-scan.o
>> xi
>> -util.o sdag-globals.o CSdagConstruct.o CEntry.o -L../bin/../lib returned
>> error
>> code 1
>> charmc exiting...
>> gmake[1]: Leaving directory
>> `/var/tmp/charm_release-2.7b2.mpi-linux-x86_64-mpicx
>> x/charm-6.1.3/mpi-linux-x86_64-mpicxx/tmp'
>> gmake[1]: *** [../bin/charmxi] Error 1
>> gmake: *** [headers] Error 2
>> -------------------------------------------------
>> Charm++ NOT BUILT. Either cd into mpi-linux-x86_64-mpicxx/tmp and try
>>
>>
>

From mille121 at illinois.edu  Fri Dec 18 17:53:04 2009
From: mille121 at illinois.edu (Phil Miller)
Date: Fri, 18 Dec 2009 17:53:04 -0600
Subject: [charm] MPI 6.1.3 build error on NCSA AC cluster
In-Reply-To: <Pine.LNX.4.63.0912181706440.25236@lisboa.ks.uiuc.edu>
References: <Pine.LNX.4.63.0912181606170.25236@lisboa.ks.uiuc.edu> 
	<81f018ac0912181430m2c727470h8c30e1942cf7e45c@mail.gmail.com> 
	<Pine.LNX.4.63.0912181706440.25236@lisboa.ks.uiuc.edu>
Message-ID: <81f018ac0912181553n218f1173ya4a9c37682cd8e53@mail.gmail.com>

On Fri, Dec 18, 2009 at 17:13, Jim Phillips <jim at ks.uiuc.edu> wrote:
>
> It's easier to just switch mpiCC to mpicxx in
> src/arch/mpi-linux-x86_64/conv-mach.sh, since that file does the right thing
> by using gcc for the native compiles.
>
> I can just define the MPICXX environment variable instead, right?

That ought to work.

> -Jim
>
>
> On Fri, 18 Dec 2009, Phil Miller wrote:
>
>> On Fri, Dec 18, 2009 at 16:17, Jim Phillips <jim at ks.uiuc.edu> wrote:
>>>
>>> Hi,
>>>
>>> I get this error building mpi-linux-x86_64-mpicxx on NCSA's AC cluster.
>>>
>>> [jphillip at ac ~]$ which mpicxx
>>> /usr/mvapich2-intel/bin/mpicxx
>>> [jphillip at ac ~]$ which icc
>>> /opt/intel/Compiler/11.1/038/bin/intel64/icc
>>>
>>> Any ideas or workaround? ?I've never seen this before. ?Looks like a yacc
>>> conflict with mvapich2, but charmxi doesn't need to be built with mpicxx.
>>
>> Try changing CMK_NATIVE_{CC,CXX,LD,LDXX} from the respective CMK_FOO
>> variables to the underlying icc/icpc in
>> src/arch/mpi-linux-x86_64/conv-mach-mpicxx.sh.
>>
>> Phil
>>
>>> -Jim
>>>
>>>
>>> ../bin/charmc -host ?-language c++ -cp ../bin/ -o charmxi xi-main.o
>>> xi-symbol.o
>>> xi-grammar.tab.o xi-scan.o xi-util.o sdag-globals.o CSdagConstruct.o
>>> CEntry.o
>>> /usr/mvapich2-intel/lib/libmpich.a(parser.o):(.bss+0x18): multiple
>>> definition of
>>> ?`yyin'
>>> xi-scan.o:(.bss+0x38): first defined here
>>> /usr/mvapich2-intel/lib/libmpich.a(parser.o):(.bss+0x20): multiple
>>> definition of
>>> ?`yyout'
>>> xi-scan.o:(.bss+0x40): first defined here
>>> ld: Warning: alignment 8 of symbol `yylval' in xi-grammar.tab.o is
>>> smaller
>>> than
>>> 32 in /usr/mvapich2-intel/lib/libmpich.a(tokens.o)
>>> Fatal Error by charmc in directory
>>> /usr/tmp/charm_release-2.7b2.mpi-linux-x86_64
>>> -mpicxx/charm-6.1.3/mpi-linux-x86_64-mpicxx/tmp
>>> ? Command mpicxx -o charmxi xi-main.o xi-symbol.o xi-grammar.tab.o
>>> xi-scan.o
>>> xi
>>> -util.o sdag-globals.o CSdagConstruct.o CEntry.o -L../bin/../lib returned
>>> error
>>> code 1
>>> charmc exiting...
>>> gmake[1]: Leaving directory
>>> `/var/tmp/charm_release-2.7b2.mpi-linux-x86_64-mpicx
>>> x/charm-6.1.3/mpi-linux-x86_64-mpicxx/tmp'
>>> gmake[1]: *** [../bin/charmxi] Error 1
>>> gmake: *** [headers] Error 2
>>> -------------------------------------------------
>>> Charm++ NOT BUILT. Either cd into mpi-linux-x86_64-mpicxx/tmp and try
>>>
>>>
>