Charm++ parallel programming system

[Fernando Stump <fernando.stump AT gmail.com>]

HI,

I was able to run ./configure but when I run make I'm get and error at the 
linking part...



Fernando-Stumps-MacBook-Pro:yafeq_non_linear fstump2$ make
make  all-recursive
Making all in yafeq
source='quadrature.cpp' object='quadrature.lo' libtool=yes \
        DEPDIR=.deps depmode=gcc /bin/sh ../config/depcomp \
        /bin/sh ../libtool --tag=CXX   --mode=compile charmc -DHAVE_CONFIG_H 
-I. -I..   -I/opt/local/include -I/Users/fstump2/lib/include 
-I/usr/lib/include  -verbose -g -default-to-aout -language c++ -seq -c -o 
quadrature.lo quadrature.cpp
libtool: compile:  charmc -DHAVE_CONFIG_H -I. -I.. -I/opt/local/include 
-I/Users/fstump2/lib/include -I/usr/lib/include -verbose -g -default-to-aout 
-language c++ -seq -c quadrature.cpp -Wp,-MD,.deps/quadrature.TPlo 
Verbose mode set
Adding file quadrature.cpp...
charmc> ----------- Module dependency search complete ------------
Compiling quadrature.cpp
charmc: Executing rm -f quadrature.o quadrature.f.o
charmc: Executing g++ -fPIC -Wno-deprecated -DCMK_SEQUENTIAL=1 
-I/Users/fstump2/myLibs/charm-6.2/bin/../include -D__CHARMC__=1 
-DHAVE_CONFIG_H -I. -I.. -I/opt/local/include -I/Users/fstump2/lib/include 
-I/usr/lib/include -g -Wp,-MD,.deps/quadrature.TPlo -c quadrature.cpp -o 
quadrature.o
charmc> No target object-- finished
libtool: compile: mv -f "quadrature.o" ".libs/quadrature.o"
source='node.cpp' object='node.lo' libtool=yes \
        DEPDIR=.deps depmode=gcc /bin/sh ../config/depcomp \
        /bin/sh ../libtool --tag=CXX   --mode=compile charmc -DHAVE_CONFIG_H 
-I. -I..   -I/opt/local/include -I/Users/fstump2/lib/include 
-I/usr/lib/include  -verbose -g -default-to-aout -language c++ -seq -c -o 
node.lo node.cpp
libtool: compile:  charmc -DHAVE_CONFIG_H -I. -I.. -I/opt/local/include 
-I/Users/fstump2/lib/include -I/usr/lib/include -verbose -g -default-to-aout 
-language c++ -seq -c node.cpp -Wp,-MD,.deps/node.TPlo 
Verbose mode set
Adding file node.cpp...
charmc> ----------- Module dependency search complete ------------
Compiling node.cpp
charmc: Executing rm -f node.o node.f.o
charmc: Executing g++ -fPIC -Wno-deprecated -DCMK_SEQUENTIAL=1 
-I/Users/fstump2/myLibs/charm-6.2/bin/../include -D__CHARMC__=1 
-DHAVE_CONFIG_H -I. -I.. -I/opt/local/include -I/Users/fstump2/lib/include 
-I/usr/lib/include -g -Wp,-MD,.deps/node.TPlo -c node.cpp -o node.o
charmc> No target object-- finished
libtool: compile: mv -f "node.o" ".libs/node.o"
source='material.cpp' object='material.lo' libtool=yes \
        DEPDIR=.deps depmode=gcc /bin/sh ../config/depcomp \
        /bin/sh ../libtool --tag=CXX   --mode=compile charmc -DHAVE_CONFIG_H 
-I. -I..   -I/opt/local/include -I/Users/fstump2/lib/include 
-I/usr/lib/include  -verbose -g -default-to-aout -language c++ -seq -c -o 
material.lo material.cpp
libtool: compile:  charmc -DHAVE_CONFIG_H -I. -I.. -I/opt/local/include 
-I/Users/fstump2/lib/include -I/usr/lib/include -verbose -g -default-to-aout 
-language c++ -seq -c material.cpp -Wp,-MD,.deps/material.TPlo 
Verbose mode set.
.
.
.
.
.
/bin/sh ../libtool --tag=CXX   --mode=link charmc  -verbose -g 
-default-to-aout -language c++ -seq  -verbose -L/opt/local/lib 
-L/Users/fstump2/lib/lib -o libyafeq.la -rpath 
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib 
quadrature.lo node.lo material.lo shape_functions.lo mapping.lo bc.lo side.lo 
element.lo equation.lo assembler.lo mesh.lo search_tree.lo enrichment.lo 
element_error.lo interactor.lo fem.lo geometric_features.lo  -lsuperlu_3.1 
-lblas -lgmp -lloki -lboost_regex-mt -lcpputils -lloki
libtool: link: charmc -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o 
.libs/libyafeq.0.dylib  .libs/quadrature.o .libs/node.o .libs/material.o 
.libs/shape_functions.o .libs/mapping.o .libs/bc.o .libs/side.o 
.libs/element.o .libs/equation.o .libs/assembler.o .libs/mesh.o 
.libs/search_tree.o .libs/enrichment.o .libs/element_error.o 
.libs/interactor.o .libs/fem.o .libs/geometric_features.o    -language 
-L/opt/local/lib -L/Users/fstump2/lib/lib /opt/local/lib/libgmp.dylib 
-lboost_regex-mt /Users/fstump2/lib/lib/libcpputils.dylib -L/usr/lib 
-lsuperlu_3.1 -lblas -lloki    -install_name  
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib/libyafeq.0.dylib
 -compatibility_version 1 -current_version 1.0 -Wl,-single_module
Fatal Error by charmc in directory 
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/yafeq
   
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib/libyafeq.0.dylib:
 file not recognized: File truncated
charmc exiting...
make[2]: *** [libyafeq.la] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2


IF I RE-RUN THE FAILED COMMAND WITH -verbose flag I get

Fernando-Stumps-MacBook-Pro:yafeq fstump2$ charmc -verbose -dynamiclib 
-Wl,-undefined -Wl,dynamic_lookup -o .libs/libyafeq.0.dylib  
.libs/quadrature.o .libs/node.o .libs/material.o .libs/shape_functions.o 
.libs/mapping.o .libs/bc.o .libs/side.o .libs/element.o .libs/equation.o 
.libs/assembler.o .libs/mesh.o .libs/search_tree.o .libs/enrichment.o 
.libs/element_error.o .libs/interactor.o .libs/fem.o 
.libs/geometric_features.o    -language -L/opt/local/lib 
-L/Users/fstump2/lib/lib /opt/local/lib/libgmp.dylib -lboost_regex-mt 
/Users/fstump2/lib/lib/libcpputils.dylib -L/usr/lib -lsuperlu_3.1 -lblas 
-lloki    -install_name  
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib/libyafeq.0.dylib
 -compatibility_version 1 -current_version 1.0 -Wl,-single_module
Verbose mode set
Adding file .libs/quadrature.o...
Adding file .libs/node.o...
Adding file .libs/material.o...
Adding file .libs/shape_functions.o...
Adding file .libs/mapping.o...
Adding file .libs/bc.o...
Adding file .libs/side.o...
Adding file .libs/element.o...
Adding file .libs/equation.o...
Adding file .libs/assembler.o...
Adding file .libs/mesh.o...
Adding file .libs/search_tree.o...
Adding file .libs/enrichment.o...
Adding file .libs/element_error.o...
Adding file .libs/interactor.o...
Adding file .libs/fem.o...
Adding file .libs/geometric_features.o...
Adding file /opt/local/lib/libgmp.dylib...
Adding file /Users/fstump2/lib/lib/libcpputils.dylib...
Adding file 
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib/libyafeq.0.dylib...
Adding file 1.0...
charmc> ----------- Module dependency search complete ------------
Compiling /opt/local/lib/libgmp.dylib
charmc: Executing rm -f libgmp.o libgmp.f.o
Compiling /Users/fstump2/lib/lib/libcpputils.dylib
charmc: Executing rm -f libcpputils.o libcpputils.f.o
Compiling 
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib/libyafeq.0.dylib
charmc: Executing rm -f libyafeq.0.o libyafeq.0.f.o
Fatal Error by charmc in directory 
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/yafeq
   
/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib/libyafeq.0.dylib:
 file not recognized: File truncated
charmc exiting...


!!!!!!!!!!!!!!!!!!!!!!

I'm not sure if charmc is trying to create or read 

/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear/lib/libyafeq.0.dylib:
 . 

I any case that fine does not exist after it finish.

Any idea?


Thanks
Fernando
On Mar 8, 2011, at 3:25 PM, Gengbin Zheng wrote:

> We did several times before with some success, but I am afraid we did
> not document the process.
> There are lots of details related to particular machine, os or compilers.
> 
> Gengbin
> 
> 
> On Tue, Mar 8, 2011 at 3:16 PM, Fernando Stump 
> <fernando.stump AT gmail.com>
>  wrote:
>> 
>> 
>> Begin forwarded message:
>> 
>> From: Fernando Stump 
>> <fernando.stump AT gmail.com>
>> Date: March 8, 2011 3:14:57 PM CST
>> To: Phil Miller 
>> <mille121 AT illinois.edu>
>> Cc: Charm Mailing List 
>> <charm AT cs.illinois.edu>
>> Subject: Re: [ppl] [charm] Compiling with automake
>> 
>> If we go on step back.
>> 
>> I want to use parfum in a a large code with few dependencies. This code is
>> currently compiled with the help of automake to create makefile. So instead
>> of creating my own makefile ( as on the examples for charm++/parfum)  I wan
>> to use automake and charmc.
>> 
>> The question then: Have anyone used and documented automake (or cmake) with
>> charmc?
>> 
>> Thanks
>> Fernando
>> 
>> 
>> 
>> On Mar 8, 2011, at 3:03 PM, Phil Miller wrote:
>> 
>> What about just disabling (i.e. commenting out or deleting) that
>> 
>> configuration test, since you know that a) you really do want to build
>> 
>> the library with charmc as the compiler, and b) charmc doesn't quite
>> 
>> behave the way its tests expect.
>> 
>> On Tue, Mar 8, 2011 at 15:00, Gengbin Zheng 
>> <zhenggb AT gmail.com>
>>  wrote:
>> 
>> hmm, ok. what about trying  with  another charmc option:
>> 
>> -language c++
>> 
>> Gengbin
>> 
>> On Tue, Mar 8, 2011 at 2:55 PM, Fernando Stump 
>> <fernando.stump AT gmail.com>
>> wrote:
>> 
>> To use -seq, make it fails on linking as described  below
>> 
>> configure:5192: charmc -verbose -g -ld++ g++ -default-to-aout -seq
>> -I/opt/local/include -I/Users/fstump2/lib/include -I/usr/lib/inc
>> 
>> lude -L/opt/local/lib -L/Users/fstump2/lib/lib conftest.cpp -lloki >&5
>> 
>> Verbose mode set
>> 
>> Adding file conftest.cpp...
>> 
>> charmc> ----------- Module dependency search complete ------------
>> 
>> Compiling conftest.cpp
>> 
>> charmc: Executing rm -f conftest.o conftest.f.o
>> 
>> charmc: Executing g++ -fPIC -Wno-deprecated -DCMK_SEQUENTIAL=1
>> -I/Users/fstump2/myLibs/charm-6.2/bin/../include -D__CHARMC__=1 -I/o
>> 
>> pt/local/include -I/Users/fstump2/lib/include -I/usr/lib/include -g -c
>> conftest.cpp -o conftest.o
>> 
>> charmc: Executing gcc -fPIC -g -L/opt/local/lib -L/Users/fstump2/lib/lib -o
>> a.out conftest.o -L/Users/fstump2/myLibs/charm-6.2/bin/
>> 
>> ../lib -lloki
>> 
>> Undefined symbols:
>> 
>> "___gxx_personality_v0", referenced from:
>> 
>>     _main in conftest.o
>> 
>>     CIE in conftest.o
>> 
>> ld: symbol(s) not found
>> 
>> collect2: ld returned 1 exit status
>> 
>> Fatal Error by charmc in directory
>> /Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear
>> 
>>  Command gcc -fPIC -g -L/opt/local/lib -L/Users/fstump2/lib/lib -o a.out
>> conftest.o -L/Users/fstump2/myLibs/charm-6.2/bin/../lib
>> 
>> -lloki returned error code 1
>> 
>> charmc exiting...
>> 
>> 
>> The error is because it tries to link with gcc instead of g++. I tried the
>> option  -ld++ g++, but it seams to be ignored
>> 
>> Thanks
>> 
>> Fernando
>> 
>> 
>> 
>> On Mar 8, 2011, at 1:28 PM, Gengbin Zheng wrote:
>> 
>> maybe use charmc -seq, it does not assume it is a charm program by
>> 
>> using "-seq" charmc compiler flag.
>> 
>> Gengbin
>> 
>> On Tue, Mar 8, 2011 at 12:49 PM, Fernando Stump
>> 
>> <fernando.stump AT gmail.com>
>>  wrote:
>> 
>> Hi,
>> 
>> I realized that this error come from the fact that I'm trying to compile a
>> pure c++ code as if it was charm++ (i.e. without the .ci)
>> 
>> Undefined symbols:
>> 
>> "_CkRegisterMainModule", referenced from:
>> 
>>     _initCharm(int, char**)in libck.a(init.o)
>> 
>> ld: symbol(s) not found
>> 
>> collect2: ld returned 1 exit status
>> 
>> My final goal is to use ParUFM, so I need to create the init() and driver()
>> function. For now I would like to compile my code such that it starts form
>> the main on my C file
>> 
>> The question is: Which language should i set on charmc, such that it 
>> compile
>> and link a plain c++ code.
>> 
>> Thanks
>> 
>> Fernando
>> 
>> On Mar 8, 2011, at 12:24 PM, Fernando Stump wrote:
>> 
>> Hi,
>> 
>> With -default-to-aout ti compiles but I get a problem to link.
>> 
>> If I try to compile a simple c++ file conftest.cpp
>> 
>> I get this
>> 
>> Fernando-Stumps-MacBook-Pro:test_charmc fstump2$ charmc -default-to-aout
>> -verbose conftest.cpp
>> 
>> Verbose mode set
>> 
>> Adding file conftest.cpp...
>> 
>> charmc> ----------- Module dependency search complete ------------
>> 
>> Compiling conftest.cpp
>> 
>> charmc: Executing rm -f conftest.o conftest.f.o
>> 
>> charmc: Executing g++ -fPIC -Wno-deprecated -DCMK_GFORTRAN
>> -I/Users/fstump2/myLibs/charm-6.2/bin/../include -D__CHARMC__=1 -c
>> conftest.cpp -o conftest.o
>> 
>> charmc: Executing g++ -fPIC -Wno-deprecated -DCMK_GFORTRAN -D__CHARMC__=1 
>> -c
>> moduleinit17035.C -o moduleinit17035.o
>> 
>> charmc> All libraries are: -L/Users/fstump2/myLibs/charm-6.2/bin/../lib
>> -I/Users/fstump2/myLibs/charm-6.2/bin/../include
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libldb-rand.o conftest.o
>> moduleinit17035.o
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libmemory-default.o
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libthreads-default.o -lck
>> -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -lm
>> 
>> charmc: Executing g++ -o a.out -L/Users/fstump2/myLibs/charm-6.2/bin/../lib
>> -I/Users/fstump2/myLibs/charm-6.2/bin/../include
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libldb-rand.o conftest.o
>> moduleinit17035.o
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libmemory-default.o
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libthreads-default.o -lck
>> -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -lm
>> 
>> Undefined symbols:
>> 
>> "_CkRegisterMainModule", referenced from:
>> 
>>     _initCharm(int, char**)in libck.a(init.o)
>> 
>> ld: symbol(s) not found
>> 
>> collect2: ld returned 1 exit status
>> 
>> Fatal Error by charmc in directory
>> /Users/fstump2/myLibs/charm-6.2/tests/charm++/test_charmc
>> 
>>  Command g++ -o a.out -L/Users/fstump2/myLibs/charm-6.2/bin/../lib
>> -I/Users/fstump2/myLibs/charm-6.2/bin/../include
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libldb-rand.o conftest.o
>> moduleinit17035.o
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libmemory-default.o
>> /Users/fstump2/myLibs/charm-6.2/bin/../lib/libthreads-default.o -lck
>> -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -lm returned error code 
>> 1
>> 
>> charmc exiting...
>> 
>> rm -f moduleinit17035.C moduleinit17035.o
>> 
>> 
>> <conftest.cpp>
>> 
>> 
>> Thanks
>> 
>> Fernando
>> 
>> On Mar 7, 2011, at 11:55 AM, Gengbin Zheng wrote:
>> 
>> try adding:  -default-to-aout to  charmc  (adding to CFLAGS, or
>> 
>> something), so that charmc produce a binary named a.out.
>> 
>> Gengbin
>> 
>> On Mon, Mar 7, 2011 at 10:57 AM, Fernando Stump 
>> <fstump2 AT illinois.edu>
>> wrote:
>> 
>> Hi,
>> 
>> I'm trying to parallelize a finite element (FE) code with ParFum. The FE
>> code uses automake to create the makefiles. I'm using g++ (gcc) to compile
>> it.
>> 
>> If I try to substitute CXX=g++ to CXX=charmc, when I call ./configure I get
>> ab error because charmc cannot create a executable. Below is the error log.
>> 
>> Is thee any manual/tutorial about using automake (or cmake) with charm++ or
>> ParFum
>> 
>> Thanks
>> 
>> Fernando
>> 
>> 
>> configure:5192:
>> /Users/fstump2/myLibs/charm-6.2/net-darwin-x86-gfortran-gcc/bin/charmc
>> -verbose -g -I/opt/local/include -I/Users/fstump2/lib/include
>> -I/usr/lib/include -L/opt/local/lib -L/Users/fstump2/lib/lib conftest.cpp
>> -lloki >&5
>> 
>> Verbose mode set
>> 
>> Adding file conftest.cpp...
>> 
>> charmc> ----------- Module dependency search complete ------------
>> 
>> Compiling conftest.cpp
>> 
>> charmc: Executing rm -f conftest.o conftest.f.o
>> 
>> charmc: Executing g++ -fPIC -Wno-deprecated -DCMK_GFORTRAN
>> -I/Users/fstump2/myLibs/charm-6.2/net-darwin-x86-gfortran-gcc/bin/../include
>> -D__CHARMC__=1 -I/opt/local/include -I/Users/fstump2/lib/include
>> -I/usr/lib/include -g -c conftest.cpp -o conftest.o
>> 
>> charmc> No target object-- finished
>> 
>> configure:5196: $? = 0
>> 
>> configure:5234: result: no
>> 
>> configure: failed program was:
>> 
>> | /* confdefs.h */
>> 
>> | #define PACKAGE_NAME "yafeq"
>> 
>> | #define PACKAGE_TARNAME "yafeq"
>> 
>> | #define PACKAGE_VERSION "0.0.1"
>> 
>> | #define PACKAGE_STRING "yafeq 0.0.1"
>> 
>> | #define PACKAGE_BUGREPORT "Alejandro Aragon 
>> <alejandro.aragon AT gmail.com>"
>> 
>> | #define PACKAGE_URL ""
>> 
>> | #define PACKAGE "yafeq"
>> 
>> | #define VERSION "0.0.1"
>> 
>> | /* end confdefs.h.  */
>> 
>> |
>> 
>> | int
>> 
>> | main ()
>> 
>> | {
>> 
>> |
>> 
>> |   ;
>> 
>> |   return 0;
>> 
>> | }
>> 
>> configure:5239: error: in
>> `/Users/fstump2/Documents/workspace/LibFEM/ssmlib/yafeq_non_linear':
>> 
>> configure:5241: error: C++ compiler cannot create executables
>> 
>> 
>> _______________________________________________
>> 
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>> 
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>> 
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>> 
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>> 
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>> 
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>> 
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>> 
>> 
>> 
>> 
>> --
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> 
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>> 
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>> 
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>> 
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>> 
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>> 
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>> 
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