Cannot build grappa applications

[rfvander]

I downloaded the latest version of grappa and am trying to build it using the instructions in build.md, but I am experiencing trouble. My environment is listed below.
[rfvander@esgmonster grappa-source]$ ruby -v
ruby 2.1.0p0 (2013-12-25 revision 44422) [x86_64-linux]
[rfvander@esgmonster grappa-source]$ cmake -version
cmake version 2.8.12.2
[rfvander@esgmonster grappa-source]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/gcc/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: /home/jrhammon/Work/GCC/gcc-4.9.2/configure --disable-multilib --enable-threads=posix --enable-checking=release --enable-__cxa_atexit --enable-languages=c,c++,fortran --with-tune=native --enable-bootstrap --enable-lto --prefix=/opt/gcc/4.9.2 --with-isl --with-cloog
Thread model: posix
gcc version 4.9.2 (GCC)
[rfvander@esgmonster Synch_p2p]$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/opt/gcc/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: /home/jrhammon/Work/GCC/gcc-4.9.2/configure --disable-multilib --enable-threads=posix --enable-checking=release --enable-__cxa_atexit --enable-languages=c,c++,fortran --with-tune=native --enable-bootstrap --enable-lto --prefix=/opt/gcc/4.9.2 --with-isl --with-cloog
Thread model: posix
gcc version 4.9.2 (GCC)
[rfvander@esgmonster grappa-source]$ mpicc -v
mpigcc for the Intel(R) MPI Library 5.1.2 for Linux*
Copyright(C) 2003-2015, Intel Corporation. All rights reserved.
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/gcc/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: /home/jrhammon/Work/GCC/gcc-4.9.2/configure --disable-multilib --enable-threads=posix --enable-checking=release --enable-__cxa_atexit --enable-languages=c,c++,fortran --with-tune=native --enable-bootstrap --enable-lto --prefix=/opt/gcc/4.9.2 --with-isl --with-cloog
Thread model: posix
gcc version 4.9.2 (GCC)
[rfvander@esgmonster grappa-source]$ mpicxx -v
mpigxx for the Intel(R) MPI Library 5.1.2 for Linux*
Copyright(C) 2003-2015, Intel Corporation. All rights reserved.
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/opt/gcc/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: /home/jrhammon/Work/GCC/gcc-4.9.2/configure --disable-multilib --enable-threads=posix --enable-checking=release --enable-__cxa_atexit --enable-languages=c,c++,fortran --with-tune=native --enable-bootstrap --enable-lto --prefix=/opt/gcc/4.9.2 --with-isl --with-cloog
Thread model: posix
gcc version 4.9.2 (GCC)

When I now follow your instructions and try to build grappa, this is what happens (no errors reported when building grappa itself)
\rm -rf build
./configure --prefix=~/grappa --cc=gcc --cxx=g++
cd build/Make+Release/
make
make install
source /home/rfvander/grappa/bin/settings.sh
cd ~/esg-prk-devel/GRAPPA/Synch_p2p
[rfvander@esgmonster Synch_p2p]$ make p2p
/opt/gcc/4.9.2/bin/g++ -O3 -std=c99 -DGRAPPA -DENABLE_RDMA_AGGREGATOR -std=c++11 -Winline -Wno-inline -mno-red-zone -O3 -g -DNDEBUG -I/home/rfvander/grappa/include -I/home/rfvander/grappa/include/Grappa -I/home/rfvander/grappa/include/Grappa/tasks -I/opt/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/include -I/usr/local/include -I../../include -c p2p.cpp
cc1plus: warning: command line option ‘-std=c99’ is valid for C/ObjC but not for C++
/opt/gcc/4.9.2/bin/g++ -o p2p -L/home/rfvander/grappa/lib -L/usr/local/lib -L/opt/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib -L/opt/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/release_mt -L/usr/lib64 -O3 -std=c99 -DGRAPPA p2p.o -Wl,-Bstatic -lGrappa -lglog -lgflags -lgraph500-generator -lboost_system -lboost_filesystem -Wl,-Bdynamic -lmpicxx -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread
/home/rfvander/grappa/lib/libglog.a(libglog_la-utilities.o): In function google::GetStackTrace(void**, int, int)': utilities.cc:(.text+0x70a): undefined reference to_Ux86_64_getcontext'
utilities.cc:(.text+0x723): undefined reference to _ULx86_64_init_local' utilities.cc:(.text+0x776): undefined reference to_ULx86_64_get_reg'
utilities.cc:(.text+0x7c6): undefined reference to `_ULx86_64_step'
collect2: error: ld returned 1 exit status
make: *** [p2p] Error 1

[nelsonje]

Weird. These symbols should come from glibc which ought to be linked with any binary you build.

Could you look at /home/rfvander/grappa/share/Grappa/grappa.mk and verify that GRAPPA_CXX is /opt/gcc/4.9.2/bin/g++?

[rfvander]

I checked and these are the related symbols in grappa.mk

#############################################################################

compiler used to build Grappa

#############################################################################

MPI header paths should automatically be included in CXXFLAGS by

CMake, so use the plain C++ compiler (but mpicxx should be fine too)

GRAPPA_CXX=/opt/gcc/4.9.2/bin/g++

MPI libraries should automatically be included in CXXFLAGS by

CMake, so use the plain C++ compiler (but mpicxx should be fine too)

GRAPPA_CC=/opt/gcc/4.9.2/bin/g++
GRAPPA_LD=/opt/gcc/4.9.2/bin/g++

[nelsonje]

Super weird. I guess try adding "-lc" to the dynamic section of the libraries in that file as a temporary fix? It should be linked be default, though....

[rfvander]

Sure, I’ll try that for now. Thanks.

From: Jacob Nelson [mailto:notifications@github.com]
Sent: Friday, April 22, 2016 2:44 PM
To: uwsampa/grappa
Cc: Van Der Wijngaart, Rob F; Author
Subject: Re: [uwsampa/grappa] Cannot build grappa applications (#278)

Super weird. I guess try adding "-lc" to the dynamic section of the libraries in that file as a temporary fix? It should be linked be default, though....

—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHubhttps://github.com//issues/278#issuecomment-213597798

[rfvander]

Sadly, no cigar. See below.

[rfvander@esgmonster Synch_p2p]$ make p2p
/opt/gcc/4.9.2/bin/g++ -O3 -std=c99 -DGRAPPA -DENABLE_RDMA_AGGREGATOR -std=c++11 -Winline -Wno-inline -mno-red-zone -O3 -g -DNDEBUG -I/home/rfvander/grappa/include -I/home/rfvander/grappa/include/Grappa -I/home/rfvander/grappa/include/Grappa/tasks -I/opt/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/include -I/usr/local/include -I../../include -c p2p.cpp
cc1plus: warning: command line option ‘-std=c99’ is valid for C/ObjC but not for C++
/opt/gcc/4.9.2/bin/g++ -o p2p -L/home/rfvander/grappa/lib -L/usr/local/lib -L/opt/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib -L/opt/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/release_mt -L/usr/lib64 -O3 -std=c99 -DGRAPPA p2p.o -Wl,-Bstatic -lGrappa -lglog -lgflags -lgraph500-generator -lboost_system -lboost_filesystem -Wl,-Bdynamic -lmpicxx -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -lc
/home/rfvander/grappa/lib/libglog.a(libglog_la-utilities.o): In function google::GetStackTrace(void**, int, int)': utilities.cc:(.text+0x70a): undefined reference to_Ux86_64_getcontext'
utilities.cc:(.text+0x723): undefined reference to _ULx86_64_init_local' utilities.cc:(.text+0x776): undefined reference to_ULx86_64_get_reg'
utilities.cc:(.text+0x7c6): undefined reference to `_ULx86_64_step'
collect2: error: ld returned 1 exit status
make: *** [p2p] Error 1

From: Jacob Nelson [mailto:notifications@github.com]
Sent: Friday, April 22, 2016 2:44 PM
To: uwsampa/grappa
Cc: Van Der Wijngaart, Rob F; Author
Subject: Re: [uwsampa/grappa] Cannot build grappa applications (#278)

Super weird. I guess try adding "-lc" to the dynamic section of the libraries in that file as a temporary fix? It should be linked be default, though....

—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHubhttps://github.com//issues/278#issuecomment-213597798

[nelsonje]

In the original build output, there was a line like:

-- Using {${BASE_C_COMPILER},${BASE_CXX_COMPILER}} to build third-party dependencies (if needed).

What did it say for this build?

[rfvander]

I didn't capture that output myself. Does Grappa store it in a log file somewhere?

[nelsonje]

There's a file CMakeCache.txt in build/Make+Release that has the values of many of these variables; send that to me through email and I'll see if I have any ideas.

[nelsonje]

It's hard to tell much from the cache file. Try rebuilding with the flags --cc=$(which gcc) --cxx=$(which g++). Perhaps it's picking up a different version of g++ when building the library?

[rfvander]

Sadly, this did not change anything.

From: Jacob Nelson [mailto:notifications@github.com]
Sent: Monday, April 25, 2016 11:20 PM
To: uwsampa/grappa
Cc: Van Der Wijngaart, Rob F; Author
Subject: Re: [uwsampa/grappa] Cannot build grappa applications (#278)

It's hard to tell much from the cache file. Try rebuilding with the flags --cc=$(which gcc) --cxx=$(which g++). Perhaps it's picking up a different version of g++ when building the library?

—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHubhttps://github.com//issues/278#issuecomment-214627618

[jeffhammond]

Related:

• libglog.pc.in should include libunwind as private dep for static linking case google/glog#57 (previously https://code.google.com/archive/p/google-glog/issues/207)
• Compilation issue on Ubuntu 13.10 with libunwind-dev installed palominolabs/protobuf-util#11

[jeffhammond]

This is fixed by adding libunwind to grappa.mk manually, e.g.

# assign to LDLIBS for automatic builds using gmake default implicit rules
GRAPPA_LDLIBS=-Wl,-Bstatic  \
    -lGrappa \
    -lglog \
    -lgflags \
    -lgraph500-generator \
    -lboost_system \
    -lboost_filesystem \
    -Wl,-Bdynamic  \
    -lmpicxx \
    -lmpifort \
    -lmpi \
    -lmpigi \
    -lunwind-x86_64 -lunwind \
    -ldl \
    -lpthread \
    -lrt

This should not be necessary.

While we are on the subject of linked libraries, why is graph500-generator linked statically with every Grappa program? Do any of the PRKs need to generate Graph500 inputs???

[Jeongseob]

I am facing the same issue. In addition, the way from @jeffhammond didn't work for me. I manually modified the build/Make+Release/util/grappa.mk, but it still generates the same error.

Linking CXX executable hello_world.exe
../../third-party/lib/libglog.a(libglog_la-utilities.o): In function `google::GetStackTrace(void**, int, int)':
utilities.cc:(.text+0x70a): undefined reference to `_Ux86_64_getcontext'
utilities.cc:(.text+0x723): undefined reference to `_ULx86_64_init_local'
utilities.cc:(.text+0x776): undefined reference to `_ULx86_64_get_reg'
utilities.cc:(.text+0x7c6): undefined reference to `_ULx86_64_step'
collect2: error: ld returned 1 exit status
make[3]: *** [applications/demos/hello_world.exe] Error 1
make[2]: *** [applications/demos/CMakeFiles/demo-hello_world.dir/all] Error 2
make[1]: *** [applications/demos/CMakeFiles/demo-hello_world.dir/rule] Error 2
make: *** [demo-hello_world] Error 2

[JackChuang]

When I was trying to compile grappa's applications, I got a HTTP 404 Not Found. It seems the link is dead. Any ideas will be appreciated.

My working env:
ubuntu14.04.3
gcc version 4.8.4

$ cd build/Make+Release
$ make

(...omitted...)
gcc.archive bin.v2/libs/test/build/gcc-4.8/release/link-static/threading-multi/libboost_unit_test_framework.a
common.copy /home/jack/grappa/grappa/build/Make+Release/third-party/lib/libboost_unit_test_framework.a
...updated 10708 targets...
[ 5%] No install step for 'third-party-boost'
[ 5%] Completed 'third-party-boost'
[ 8%] Built target third-party-boost
[ 8%] Performing download step (download, verify and extract) for 'third-party-gflags'
-- downloading...
src='http://gflags.googlecode.com/files/gflags-2.0-no-svn-files.tar.gz'
dst='/home/jack/grappa/grappa/build/Make+Release/third-party/build/gflags/src/gflags-2.0-no-svn-files.tar.gz'
timeout='none'
CMake Error at /home/jack/grappa/grappa/build/Make+Release/third-party/build/stamps/gflags/download-third-party-gflags.cmake:22 (message):
error: downloading
'http://gflags.googlecode.com/files/gflags-2.0-no-svn-files.tar.gz' failed

status_code: 22
status_string: "HTTP response code said error"
log: Hostname was NOT found in DNS cache
Trying 173.194.205.82...

Connected to gflags.googlecode.com (173.194.205.82) port 80 (#0)

GET /files/gflags-2.0-no-svn-files.tar.gz HTTP/1.1

User-Agent: curl/7.35.0

Host: gflags.googlecode.com

Accept: /

The requested URL returned error: 404 Not Found

Closing connection 0

make[2]: *** [third-party/build/stamps/gflags/third-party-gflags-download] Error 1
make[1]: *** [third-party/CMakeFiles/third-party-gflags.dir/all] Error 2
make: *** [all] Error 2
root@Jack-desktop:/home/jack/grappa/grappa/build/Make+Release#
root@Jack-desktop:/home/jack/grappa/grappa/build/Make+Release#