Charm++ parallel programming system

[Phil Miller <mille121 AT illinois.edu>]

Hi Cletus,

On Fri, Oct 9, 2015 at 11:51 AM, Asuquo, Cletus <cletus.asuquo AT usask.ca> wrote:

Please, pardon my ignorance, what do you mean by 'main line version of Charm++'? I have downloaded Charm dirrectly from http://charmplusplus.org/download/​, yet it still bring same error while trying to build.

If you download the 'Latest Dev Version'/'Nightly Snapshot' instead of the 6.6.1 release, or follow the instructions to clone our git repository, that code should work.

Please excuse the slow response.

Phil

Kind regards,

Cletus

---

From: unmobile AT gmail.com <unmobile AT gmail.com> on behalf of Phil Miller <mille121 AT illinois.edu>
Sent: October 9, 2015 10:15 AM
To: Asuquo, Cletus

Subject: Re: [charm] Error while building Charm

 

This error (only arising with newer compilers) was fixed in our development version a few months ago. I'd suggest building against a main line version of Charm++, since it's in a pretty stable state as we prepare a release.

On Fri, Oct 9, 2015 at 11:07 AM, Asuquo, Cletus <cletus.asuquo AT usask.ca> wrote:

Hi Phil, 

Below is the entire output while trying to build.

Copying src/scripts/Makefile to multicore-linux64/tmp

Soft-linking over bin

Soft-linking over lib

Soft-linking over lib_so

Soft-linking over include

Soft-linking over tmp

Generating multicore-linux64/tmp/conv-mach-pre.sh

Performing 'make basics OPTS= QUIET= CONFIG_OPTS=' in multicore-linux64/tmp

Makefile:1083: Variable OPTS is defined to an empty string. Are you sure this is what you want?

make charmxi

Makefile:1083: Variable OPTS is defined to an empty string. Are you sure this is what you want?

./configure

Error checking is enabled

Statistics collection is enabled

Charm tracing is enabled

Charm tracing communication thread is disabled

CharmDebug is enabled

Charm record/replay is enabled

CCS is enabled

Charm control point is enabled

Charm LB user data is disabled

Setting load balancing timer type as 'double'

checking machine name... multicore-linux64

checking "cp command as"... cp -p

checking "C++ compiler as"... "g++  -D_REENTRANT -m64     -U_FORTIFY_SOURCE -fno-stack-protector "

checking "whether C++ compiler works"... "ok"

checking "C++ linker as"... "g++  -D_REENTRANT -m64   -D_REENTRANT -m64  -rdynamic    "

checking "whether linker works"... "ok"

checking "Native C++ compiler as"... "g++  -D_REENTRANT -m64   -D_REENTRANT -m64 -fPIC "

checking "Sequential C++ compiler as"... "g++  -D_REENTRANT -m64   -D_REENTRANT -m64 -fPIC "

checking "whether compiler accept -fno-stack-protector"... "ok"

Setting charm++ envelope refnum field to unsigned short

Configuring support for message priorities of arbitrary size (bitvectors)

checking "whether compiler generates code for 64-bit"... "yes"

checking "whether compiler supports std::alignment_of"... "no"

checking "whether has values.h "... "no"

checking "whether has stdint.h "... "yes"

checking "whether has malloc.h "... "no"

checking "whether has alloca.h "... "yes"

checking "whether has regex.h "... "yes"

checking "whether long long works"... "yes"

checking "whether __int64 works"... "no"

checking "whether __int128 (128-bit integer) works"... "no"

checking "whether __int128_t (128-bit integer) works"... "yes"

checking "whether long double works"... "yes"

checking "whether ucontext has FPU pointer"... "no"

checking "whether ucontext has pointer (v_regs) of vector type"... "no"

checking "whether ibverbs ibv_port_attr has link_layer field"... "no"

checking "whether inline works in C"... "yes"

checking "whether C++ signed char and char differ"... "yes"

checking "whether C++ allows declaration of varsize array"... "yes"

checking "whether typeinfo/typeid works"... "ok"

checking "whether std::iterator_traits is defined"... "ok"

checking "whether std::distance is defined"... "ok"

checking "whether std::inserter is defined"... "ok"

checking "whether std::unordered_map is defined"... "no"

checking "whether anon structs are permitted"... "yes"

checking "whether operator delete can be overloaded in same class"... "ok"

checking "whether offsetof is defined"... "yes"

checking "whether GCC x86 assembly works"... "yes"

checking "whether GCC x86 assembly for atomic increment works"... "yes"

checking "whether GCC IA64 assembly works"... "no"

checking "whether asm eieio assembly works"... "no"

checking "whether __thread (Thread Local Storage) is supported"... "no"

checking "whether synchronization primitives (__sync_add_and_fetch) works in C"... "no"

checking "whether synchronization primitives (__sync_synchronize) works in C"... "no"

checking "whether fence intrinsic primitives (__builtin_Xfence_ia32) works in C"... "no"

checking "whether switching TLS register (64-bit) is supported"... "no"

checking "whether getrusage accepts RUSAGE_THREAD"... "no"

checking "whether has asctime"... "yes"

checking "whether has log2"... "yes"

checking "whether has sqrtf"... "yes"

checking "whether has fabsf"... "yes"

checking "whether has mkstemp"... "yes"

checking "whether has system"... "yes"

checking "whether has sync()"... "yes"

checking "whether has fsync()"... "yes"

checking "whether has fdatasync()"... "no"

checking "whether has sbrk"... "yes"

checking "whether has _setjmp/_longjmp"... "yes"

checking "whether has mstats"... "no"

checking "whether has mallinfo"... "no"

checking "whether has popen"... "yes"

checking "whether has poll"... "yes"

checking "whether has getpagesize"... "yes"

checking "whether has getpid"... "yes"

checking "whether has kill"... "yes"

checking "whether has setpriority"... "yes"

checking "whether to use signal-safe system() "... "no"

checking "whether sched_setaffinity call exists"... "no"

checking "whether pthread_setaffinity_np call exists"... "no"

checking "whether pthread_spin_lock exists"... "no"

checking "whether bindprocessor call exists"... "no"

checking "whether dlopen links without -ldl"... "yes"

checking "whether dlopen links with -ldl"... "yes"

checking "whether gethostname call exists"... "yes"

checking "whether getProcAddress works"... "no"

checking "whether has socklen_t"... "yes"

checking "whether getifaddrs call exists"... "yes"

checking "whether the mmap() syscall exists"... "yes"

checking "whether mmap() accepts MAP_ANON"... "yes"

checking "whether mmap() accepts MAP_NORESERVE"... "yes"

checking "whether has get_myaddress"... "no"

checking "whether has mprotect"... "yes"

checking "whether glibc backtrace works"... "yes"

checking "whether has sleep "... "yes"

checking "whether has usleep "... "yes"

checking "whether personality() and ADDR_NO_RANDOMIZE exist"... "no"

checking "whether has zlib"... "yes"

checking "whether has elf.h "... "no"

checking "whether has Multiprocessing.h for Apple "... "no"

checking "whether ntohl is available"... "yes"

checking "whether has libjpeg"... "no"

checking "whether Python is installed"... "yes"

checking "whether can build shared library"... "no"

checking for sync... sync 

checking "F77 compiler as"... "ifort "

checking "whether Fortran 77 compiler works"... "yes"

checking "F90 compiler as"... "ifort "

checking "whether Fortran 90 compiler works"... "yes"

checking subroutine name used by Fortran 90 compiler... ONESCORE

checking Fortran 90 mod name is capital... "no"

checking Fortran 90 mod name extension... "mod"

configure: creating ./config.status

config.status: creating libs/ck-libs/ampi/ampiCC

config.status: creating libs/ck-libs/ampi/ampirun

config.status: creating conv-autoconfig.h

config.status: executing config-cleanup commands

config.status: executing default commands

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o xi-main.o ../../src/xlat-i/xi-main.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o xi-symbol.o ../../src/xlat-i/xi-symbol.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o xi-grammar.tab.o ../../src/xlat-i/xi-grammar.tab.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I. -DYY_NEVER_INTERACTIVE   -c -o xi-scan.o ../../src/xlat-i/xi-scan.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o xi-util.o ../../src/xlat-i/xi-util.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o sdag-globals.o ../../src/xlat-i/sdag/sdag-globals.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o CSdagConstruct.o ../../src/xlat-i/sdag/CSdagConstruct.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o CEntry.o ../../src/xlat-i/sdag/CEntry.C

../bin/charmc -host  -I../../src/xlat-i/ -I../../src/xlat-i/sdag/ -I.   -c -o CParsedFile.o ../../src/xlat-i/sdag/CParsedFile.C

../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 CParsedFile.o

Undefined symbols:

  "xi::AstChildren<xi::Member>::push_back(xi::Member*)", referenced from:

      xi::Chare::Chare(int, unsigned int, xi::NamedType*, xi::TypeList*, xi::AstChildren<xi::Member>*)in xi-symbol.o

      xi::Chare::Chare(int, unsigned int, xi::NamedType*, xi::TypeList*, xi::AstChildren<xi::Member>*)in xi-symbol.o

      xi::Chare::genDecls(xi::XStr&)    in xi-symbol.o

ld: symbol(s) not found

collect2: ld returned 1 exit status

Fatal Error by charmc in directory /Users/cletus/NAMD_CVS-2015-10-09_Source/charm-6.6.1/multicore-linux64/tmp

   Command g++ -D_REENTRANT -m64 -D_REENTRANT -m64 -fPIC -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 CParsedFile.o -L../bin/../lib returned error code 1

charmc exiting...

make[1]: *** [../bin/charmxi] Error 1

make: *** [headers] Error 2

​Regards,

Cletus

---

From: unmobile AT gmail.com <unmobile AT gmail.com> on behalf of Phil Miller <mille121 AT illinois.edu>
Sent: October 9, 2015 9:57 AM
To: Asuquo, Cletus
Cc: charm AT cs.uiuc.edu
Subject: Re: [charm] Error while building Charm

 

Hi Cletus,

Could you please send us the several lines of error output preceding that failure? Just knowing that linking failed doesn't give us enough to diagnose the problem.

Phil

On Fri, Oct 9, 2015 at 10:54 AM, Asuquo, Cletus <cletus.asuquo AT usask.ca> wrote:

Dear Support,

While trying to compile NAMD, I had to build charm++. I issued the command

./build charm++ multicore-linux64 --with-production

But it exited with the error 

Fatal Error by charmc in directory /Users/cletus/NAMD_CVS-2015-10-09_Source/charm-6.6.1/multicore-linux64/tmp

   Command g++ -D_REENTRANT -m64 -D_REENTRANT -m64 -fPIC -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 CParsedFile.o -L../bin/../lib returned error code 1

charmc exiting...

​

I don't have any clue how to fix this, but I need to use the program urgently. Can you please help me?

Regards,

Cletus Asuquo