[Boost-build] Help building Boost (error with multi-thread)

Subject: [Boost-build] Help building Boost (error with multi-thread)
From: Dr. Samir Naboulsi (naboulsk.ctr_at_[hidden])
Date: 2015-04-07 12:01:28

Greeting

  I am new to Boost, and I am having problem building MPI version using 
gnu compiler and SGI MPT on an HPC SGI Ice X - 1.5
  PFLOPS system. I am getting the following error:

"
gcc.link.dll 
bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/libboost_mpi.so.1.57.0
/usr/bin/ld: mpi_sgi_prior_func: TLS definition in 
/opt/sgi/mpt/mpt-2.11/lib/libmpi_mt.so section .tbss mismatches non-TLS 
definition in /opt/sgi/mpt/mpt-2.11/lib/libmpi.so section .bss
/opt/sgi/mpt/mpt-2.11/lib/libmpi_mt.so: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
"

Also, not sure how to turn icu even though I used
"--with-icu   --withicu=..."

I am using the following user-config.jam:

using gcc : 4.7.3 : /app/gmpapp/gcc/platform/gcc-4.7.3/bin/g++ ;
using mpi : : <find-shared-library>mpi  <find-shared-library>mpi++ 
<find-shared-library>mpi_mt  <find-shared-library>sma 
<find-shared-library>mpi_bpheap  <find-shared-library>pmi2mpt 
<find-shared-library>xmpi  <find-shared-library>mpi_lustre 
<find-shared-library>mpi_panfs <find-shared-library>mpi_f08_intel 
<find-shared-library>mpi++abi1002 ;

and the following to build:

./bootstrap.sh 
--with-libraries=atomic,chrono,container,context,coroutine,date_time,exception,filesystem,graph,graph_parallel,iostreams,locale,log,math,mpi,program_options,python,random,regex,serialization,signals,system,test,thread,timer,wave 

--with-icu 
--with-icu=/work1/home/naboulsk/SINSTAL/DLPackage/Gicu/build 
--with-python=python 
--with-python-root=/app/wpostool/COST/python-2.6.8 
--prefix=/work1/home/naboulsk/SINSTAL/DLPackage/boost_1.57
--exec-prefix=/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57 
--libdir=/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib 
--includedir=/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/include

./b2 --user-config=user-config.jam --debug-configuration install

I am getting the following out put:

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

otice: found boost-build.jam at 
/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/boost-build.jam
notice: loading Boost.Build from 
/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src
notice: Searching '/etc' '/home/naboulsk' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src' 
'/usr/share/boost-build' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/kernel' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/util' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/build' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/tools' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/contrib' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/.' 
for site-config configuration file 'site-config.jam'.
notice: Configuration file 'site-config.jam' not found in '/etc' 
'/home/naboulsk' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src' 
'/usr/share/boost-build' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/kernel' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/util' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/build' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/tools' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/contrib' 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/tools/build/src/.'.
notice: Loading explicitly specified user configuration file:
     /work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/user-config.jam
notice: Searching 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P' for user-config 
configuration file 'user-config.jam'.
notice: Loading user-config configuration file 'user-config.jam' from 
'/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P'.
notice: will use '/app/gmpapp/gcc/platform/gcc-4.7.3/bin/g++' for gcc, 
condition <toolset>gcc-4.7.3
notice: using gcc libraries :: <toolset>gcc-4.7.3 :: 
/app/gmpapp/gcc/platform/gcc-4.7.3/bin 
/app/gmpapp/gcc/platform/gcc-4.7.3/lib 
/app/gmpapp/gcc/platform/gcc-4.7.3/lib32 
/app/gmpapp/gcc/platform/gcc-4.7.3/lib64
notice: using gcc archiver :: <toolset>gcc-4.7.3 :: ar
notice: using gcc ranlib :: <toolset>gcc-4.7.3 :: ranlib
warning: toolset gcc initialization: can not find tool windres
warning: initialized from 
/work1/home/naboulsk/SINSTAL/DLPackage/Gboost_1_57_0_P/user-config.jam:1
notice: using rc compiler :: <toolset>gcc-4.7.3 :: as
MPI build features:
<find-shared-library>mpi <find-shared-library>mpi++ 
<find-shared-library>mpi_mt <find-shared-library>sma 
<find-shared-library>mpi_bpheap <find-shared-library>pmi2mpt 
<find-shared-library>xmpi <find-shared-library>mpi_lustre 
<find-shared-library>mpi_panfs <find-shared-library>mpi_f08_intel 
<find-shared-library>mpi++abi1002
MPI launcher: mpirun -np
====================================================
notice: Searching '.' for project-config configuration file 
'project-config.jam'.
notice: Loading project-config configuration file 'project-config.jam' 
from '.'.
notice: [python-cfg] Configuring python...
notice: [python-cfg]   user-specified version: "2.6"
notice: [python-cfg]   user-specified cmd-or-prefix: 
"/app/wpostool/COST/python-2.6.8"
notice: [python-cfg] Checking interpreter command 
"/app/wpostool/COST/python-2.6.8/bin/python2.6"...
notice: [python-cfg] running command 
'/app/wpostool/COST/python-2.6.8/bin/python2.6 -c "from sys import *; 
print('version=%d.%d\nplatform=%s\nprefix=%s\nexec_prefix=%s\nexecutable=%s' 
% 
(version_info[0],version_info[1],platform,prefix,exec_prefix,executable))" 
2>&1'
notice: [python-cfg] ...requested configuration matched!
notice: [python-cfg] Details of this Python configuration:
notice: [python-cfg]   interpreter command: 
"/app/wpostool/COST/python-2.6.8/bin/python2.6"
notice: [python-cfg]   include path: 
"/app/wpostool/COST/python-2.6.8/include/python2.6"
notice: [python-cfg]   library path: 
"/app/wpostool/COST/python-2.6.8/lib/python2.6/config" 
"/app/wpostool/COST/python-2.6.8/lib"
notice: [zlib] Using pre-installed library
notice: [zlib] Condition
notice: iostreams: using prebuilt bzip2
Performing configuration checks

     - 32-bit                   : no  (cached)
     - 64-bit                   : yes (cached)
     - arm                      : no  (cached)
     - mips1                    : no  (cached)
     - power                    : no  (cached)
     - sparc                    : no  (cached)
     - x86                      : yes (cached)
     - lockfree boost::atomic_flag : yes (cached)
     - has_icu builds           : no  (cached)
     - zlib                     : yes (cached)
     - iconv (libc)             : yes (cached)
     - icu                      : no  (cached)
     - icu (lib64)              : no  (cached)
     - compiler-supports-ssse3  : yes (cached)
     - compiler-supports-avx2   : no  (cached)
     - gcc visibility           : yes (cached)
     - long double support      : yes (cached)
     - zlib                     : yes (cached)

Component configuration:

     - atomic                   : building
     - chrono                   : building
     - container                : building
     - context                  : building
     - coroutine                : building
     - date_time                : building
     - exception                : building
     - filesystem               : building
     - graph                    : building
     - graph_parallel           : building
     - iostreams                : building
     - locale                   : building
     - log                      : building
     - math                     : building
     - mpi                      : building
     - program_options          : building
     - python                   : building
     - random                   : building
     - regex                    : building
     - serialization            : building
     - signals                  : building
     - system                   : building
     - test                     : building
     - thread                   : building
     - timer                    : building
     - wave                     : building

...patience...
...patience...
...patience...
...patience...
...patience...
...patience...
...found 35245 targets...
...updating 11 targets...

gcc.link.dll 
bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/libboost_mpi.so.1.57.0
/usr/bin/ld: mpi_sgi_prior_func: TLS definition in 
/opt/sgi/mpt/mpt-2.11/lib/libmpi_mt.so section .tbss mismatches non-TLS 
definition in /opt/sgi/mpt/mpt-2.11/lib/libmpi.so section .bss
/opt/sgi/mpt/mpt-2.11/lib/libmpi_mt.so: could not read symbols: Bad value
collect2: error: ld returned 1 exit status

     "/app/gmpapp/gcc/platform/gcc-4.7.3/bin/g++"    -o 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/libboost_mpi.so.1.57.0" 
-Wl,-h -Wl,libboost_mpi.so.1.57.0 -shared -Wl,--start-group 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/broadcast.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/communicator.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/computation_tree.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/content_oarchive.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/environment.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/exception.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/graph_communicator.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/group.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/intercommunicator.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/mpi_datatype_cache.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/mpi_datatype_oarchive.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/packed_iarchive.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/packed_oarchive.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/packed_skeleton_iarchive.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/packed_skeleton_oarchive.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/point_to_point.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/request.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/text_skeleton_oarchive.o" 
"bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/timer.o" 
"bin.v2/libs/serialization/build/gcc-4.7.3/release/threading-multi/libboost_serialization.so.1.57.0" 
  -Wl,-Bstatic  -Wl,-Bdynamic -lmpi -lmpi++ -lmpi++abi1002 -lmpi_bpheap 
-lmpi_f08_intel -lmpi_lustre -lmpi_mt -lmpi_panfs -lpmi2mpt -lsma -lxmpi 
-lrt -Wl,--end-group -pthread

...failed gcc.link.dll 
bin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi/libboost_mpi.so.1.57.0...
...skipped 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_mpi.so.1.57.0 
for lack of 
<pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>libboost_mpi.so.1.57.0...
...skipped 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_mpi.so 
for lack of 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_mpi.so.1.57.0...
...skipped 
<pbin.v2/libs/graph_parallel/build/gcc-4.7.3/release/threading-multi>libboost_graph_parallel.so.1.57.0 
for lack of 
<pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>libboost_mpi.so.1.57.0...
...skipped 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_graph_parallel.so.1.57.0 
for lack of 
<pbin.v2/libs/graph_parallel/build/gcc-4.7.3/release/threading-multi>libboost_graph_parallel.so.1.57.0...
...skipped 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_graph_parallel.so 
for lack of 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_graph_parallel.so.1.57.0...
...skipped 
<pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>libboost_mpi_python.so.1.57.0 
for lack of 
<pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>libboost_mpi.so.1.57.0...
...skipped 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_mpi_python.so.1.57.0 
for lack of 
<pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>libboost_mpi_python.so.1.57.0...
...skipped 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_mpi_python.so 
for lack of 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>libboost_mpi_python.so.1.57.0...
...skipped 
<pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>mpi.so for 
lack of 
<pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>libboost_mpi_python.so.1.57.0...
...skipped 
<p/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib>mpi.so for 
lack of <pbin.v2/libs/mpi/build/gcc-4.7.3/release/threading-multi>mpi.so...
...failed updating 1 target...
...skipped 10 targets...

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

At the end it only built 12540 targets :

common.copy 
/work1/home/naboulsk/SINSTAL/BuildProjGNU/boost_1.57/lib/libboost_test_exec_monitor.a
...failed updating 1 target...
...skipped 10 targets...
...updated 12540 targets...