[parsec-users] The Beta Release of PARSEC 3.0

Yungang Bao ybao at CS.Princeton.EDU
Wed Sep 19 08:07:30 EDT 2012


Hi Juan,

Thank you very much. We appreciate your effort.

Best regards,
Yungang

On Sep 18, 2012, at 10:59 AM, Juan Manuel Cebrián González <juanmc at idi.ntnu.no> wrote:

> Hi. Several problems and solutions on this email. Solutions make all benchmarks in group "pthread" compile, but I'm not completely sure if they actually work, will test that later. 
> 
> PD: Long email :).
> 
> 
> ******************************
> ****************************************************************
> 
> PROBLEM:
> 
> /pkg/libs/ssl Compilation error on modern GCC (in my case 4.7) (don't have the log right now, but should be in another mail in the mail-list https://lists.cs.princeton.edu/pipermail/parsec-users/2012-September/001417.html)
> 
> 
> SOLUTION:
> 
> Update SSL to version OpenSSL 1.0.1c
> 
> cd pkgs/libs/ssl
> mv src src_old
> wget http://www.openssl.org/source/openssl-1.0.1c.tar.gz
> tar -xzvf openssl-1.0.1c.tar.gz
> openssl-1.0.1c/ src
> rm /src/Makefile
> mv /src/config /src/configure
> 
> **********************************************************************************************
> 
> PROBLEM:
> 
> [PARSEC] [---------- Building package parsec.dedup ----------]
> [PARSEC] Copying source code of package parsec.dedup.
> ...........
> encoder.o: In function `Encode':
> /home/jcebrian/parsec-3.0_gcc_47/pkgs/kernels/dedup/obj/amd64-linux.gcc-hooks/encoder.c:1409: undefined reference to `S_ISREG'
> collect2: error: ld returned 1 exit status
> make: *** [dedup] Error 1
> [PARSEC] Error: 'env version=pthreads CFLAGS=-I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/ssl/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include LDFLAGS=-L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/ssl/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/extras/gcc-4.7.0/lib64 -L/home/jcebrian/extras/gcc-4.7.0/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/energy_lib/lib -L/home/jcebrian/extras/likwid/lib /usr/bin/make' failed.
> 
> 
> SOLUTION:
> 
> Edit pkgs/kernels/dedup/src/encoder.c
> 
> + #include <sys/stat.h>
> 
> 
> 
> **********************************************************************************************
> 
> PROBLEM:
> 
> [PARSEC] [---------- Building package parsec.netdedup ----------]
> [PARSEC] Removing old build directory.
> [PARSEC] Copying source code of package parsec.netdedup.
> [PARSEC] Running 'env version=pthreads CFLAGS=-I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/ssl/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include LDFLAGS=-L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/ssl/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/extras/gcc-4.7.0/lib64 -L/home/jcebrian/extras/gcc-4.7.0/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/energy_lib/lib -L/home/jcebrian/extras/likwid/lib /usr/bin/make':
> /usr/bin/make -C server
> ........
> /home/jcebrian/extras/gcc-4.7.0/bin/gcc -c -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/ssl/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include -O0 -g -Wall -fno-strict-aliasing -D_XOPEN_SOURCE=600 -DENABLE_PARSEC_UPTCPIP -DENABLE_GZIP_COMPRESSION -DENABLE_PTHREADS -lpthread encoder.c -o encoder.o
> encoder.c:64:26: fatal error: uptcp_socket.h: No such file or directory
> compilation terminated.
> make[1]: *** [encoder.o] Error 1
> make[1]: Leaving directory `/home/jcebrian/parsec-3.0_gcc_47/pkgs/netapps/netdedup/obj/amd64-linux.gcc-hooks/server'
> make: *** [server] Error 2
> [PARSEC] Error: 'env version=pthreads CFLAGS=-I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/ssl/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include LDFLAGS=-L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/ssl/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/extras/gcc-4.7.0/lib64 -L/home/jcebrian/extras/gcc-4.7.0/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/energy_lib/lib -L/home/jcebrian/extras/likwid/lib /usr/bin/make' failed.
> 
> SOLUTION:
> 
> Edit: /pkgs/netapps/netdedup/parsec/gcc-hooks.bldconf
> 
> Modify: build_deps="hooks ssl zlib" --> build_deps="hooks uptcpip ssl zlib"
> 
> ***************************************************************************************************
> 
> PROBLEM:
> 
> [PARSEC] [---------- Building package parsec.netstreamcluster ----------]
> [PARSEC] Copying source code of package parsec.netstreamcluster.
> [PARSEC] Running 'env version=pthreads CXXFLAGS=-I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -fpermissive -fno-exceptions -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include LDFLAGS=-L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/extras/gcc-4.7.0/lib64 -L/home/jcebrian/extras/gcc-4.7.0/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/energy_lib/lib -L/home/jcebrian/extras/likwid/lib /usr/bin/make':
> /usr/bin/make -C server
> make[1]: Entering directory `/home/jcebrian/parsec-3.0_gcc_47/pkgs/netapps/netstreamcluster/obj/amd64-linux.gcc-hooks/server'
> /home/jcebrian/extras/gcc-4.7.0/bin/g++ -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -fpermissive -fno-exceptions -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include -DENABLE_THREADS -lpthread -DENABLE_PARSEC_UPTCPIP -c streamcluster.cpp
> streamcluster.cpp: In function 'void* receive_from_client(void*)':
> streamcluster.cpp:1898:14: error: 'usleep' was not declared in this scope
> streamcluster.cpp: In function 'void streamCluster(PStream*, long int, long int, int, long int, long int, char*)':
> streamcluster.cpp:2194:12: error: 'usleep' was not declared in this scope
> make[1]: *** [streamcluster.o] Error 1
> make[1]: Leaving directory `/home/jcebrian/parsec-3.0_gcc_47/pkgs/netapps/netstreamcluster/obj/amd64-linux.gcc-hooks/server'
> make: *** [server] Error 2
> [PARSEC] Error: 'env version=pthreads CXXFLAGS=-I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -fpermissive -fno-exceptions -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include LDFLAGS=-L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/uptcpip/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/extras/gcc-4.7.0/lib64 -L/home/jcebrian/extras/gcc-4.7.0/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/energy_lib/lib -L/home/jcebrian/extras/likwid/lib /usr/bin/make' failed.
> 
> 
> SOLUTION:
> 
> Edit: /pkgs/netapps/netdedup/parsec/gcc-hooks.bldconf
> Modify: build_deps="hooks" --> build_deps="hooks uptcpip"
> 
> Edit: /pkgs/netapps/netstreamcluster/src/server/streamcluster.cpp
> 
> + #include <unistd.h>
> 
> 
> *************************************************************************************
> 
> PROBLEM:
> 
> [PARSEC] [---------- Building package parsec.raytrace ----------]
> [PARSEC] Copying source code of package parsec.raytrace.
> ...........
> 
> cd /home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL && /home/jcebrian/extras/gcc-4.7.0/bin/g++   -DTHIS_IS_CMAKE -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/mesa/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -fpermissive -fno-exceptions -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include -fexceptions -fno-strict-aliasing -fno-align-labels -DNDEBUG -D_MM_NO_ALIGN_CHECK  -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/libs/mesa/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL/common -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL/BVH -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/SG -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/LRT/include -I/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/LRT   -D__jcebrian__ -o CMakeFiles/RTTL.dir/common/MapOptions.o -c /home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL/common/MapOptions.cxx
> /home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL/common/MapOptions.cxx: In member function 'bool RTTL::MapOptions::parse(int, const char**, bool)':
> /home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL/common/MapOptions.cxx:326:57: error: 'access' was not declared in this scope
> /home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL/common/MapOptions.cxx: In member function 'bool RTTL::MapOptions::parse_file(const char*)':
> /home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks/RTTL/common/MapOptions.cxx:454:28: error: 'access' was not declared in this scope
> make[2]: *** [RTTL/CMakeFiles/RTTL.dir/common/MapOptions.o] Error 1
> make[2]: Leaving directory `/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks'
> make[1]: *** [RTTL/CMakeFiles/RTTL.dir/all] Error 2
> make[1]: Leaving directory `/home/jcebrian/parsec-3.0_gcc_47/pkgs/apps/raytrace/obj/amd64-linux.gcc-hooks'
> make: *** [all] Error 2
> [PARSEC] Error: 'env version=pthreads CXXFLAGS=-I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/mesa/inst/amd64-linux.gcc-hooks/include -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -fpermissive -fno-exceptions -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include -fexceptions -fno-strict-aliasing -fno-align-labels -DNDEBUG -D_MM_NO_ALIGN_CHECK LDFLAGS=-L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/mesa/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/extras/gcc-4.7.0/lib64 -L/home/jcebrian/extras/gcc-4.7.0/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/energy_lib/lib -L/home/jcebrian/extras/likwid/lib LIBS= -pthread -lhooks -lenergy -llikwid -lm -lGL -lGLU -lXmu -lXext -lXau -lX11 -ldl -lpthread /usr/bin/make' failed.
> 
> SOLUTION:
> 
> Edit: /pkgs/apps/raytrace/src/RTTL/common/MapOptions.hxx
> 
> + #include <unistd.h>
> 
> ************************************************************************************************************************************************
> 
> [PARSEC] [========== Building package parsec.vips [1] ==========]
> [PARSEC] [---------- Analyzing package parsec.vips ----------]
> [PARSEC] parsec.vips depends on: hooks glib libxml2 zlib
> [PARSEC] [---------- Analyzing package parsec.hooks ----------]
> [PARSEC] Package parsec.hooks already exists, proceeding.
> [PARSEC] [---------- Analyzing package parsec.glib ----------]
> [PARSEC] parsec.glib does not depend on any other packages.
> [PARSEC] [---------- Building package parsec.glib ----------]
> [PARSEC] Running 'env /home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/glib/src/configure --disable-shared --enable-threads --with-threads=posix --prefix=/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/glib/inst/amd64-linux.gcc-hooks':
> checking for a BSD-compatible install... /home/jcebrian/parsec-3.0_gcc_47/bin/../bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> ............
> checking for unistd.h... yes
> checking for inflate in -lz... no
> configure: error: *** Working zlib library and headers not found ***
> [PARSEC] Error: 'env /home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/glib/src/configure --disable-shared --enable-threads --with-threads=posix --prefix=/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/glib/inst/amd64-linux.gcc-hooks' failed.
> 
> 
> SOLUTION:
> 
> Edit: /pkgs/libs/glib/parsec/gcc.bldconf
> 
> + build_deps="zlib"
> + build_env="CFLAGS=\"-I${PARSECDIR}/pkgs/libs/zlib/inst/${PARSECPLAT}/include ${CFLAGS}\" LDFLAGS=\"-L${PARSECDIR}/pkgs/libs/zlib/inst/${PARSECPLAT}/lib ${LDFLAGS}\""
> 
> 
> 
> ************************************************************************************************************************************************
> 
> [PARSEC] [========== Building package splash2.radiosity [2] ==========]
> [PARSEC] [---------- Analyzing package splash2.radiosity ----------]
> [PARSEC] splash2.radiosity depends on:  hooks
> [PARSEC] [---------- Analyzing package parsec.hooks ----------]
> [PARSEC] Package parsec.hooks already exists, proceeding.
> [PARSEC] [---------- Building package splash2.radiosity ----------]
> [PARSEC] Copying source code of package splash2.radiosity.
> [PARSEC] Running 'env version=IN_PARSEC /usr/bin/make':
> m4 -Ulen -Uindex ../../../../null_macros/c.m4.null.pthread model.H > model.h
> .....
> make[1]: Leaving directory `/home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/glibps'
> gcc -I./glibdumb -I./glibps -I/usr/local/include -g  -g -w -lpthread -lm  rad_main.o patchman.o elemman.o taskman.o modelman.o smallobj.o display.o visible.o rad_tools.o room_model.o  ./glibdumb/glib.a glibps/glibps.a -o radiosity
> rad_main.o: In function `main':
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/rad_main.c:1334: undefined reference to `pthread_create'
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/rad_main.c:1350: undefined reference to `pthread_join'
> rad_main.o: In function `start_radiosity':
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/rad_main.c:1520: undefined reference to `pthread_create'
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/rad_main.c:1536: undefined reference to `pthread_join'
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/rad_main.c:1653: undefined reference to `pthread_create'
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/rad_main.c:1743: undefined reference to `pthread_join'
> smallobj.o: In function `vector_length':
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/smallobj.c:1162: undefined reference to `sqrt'
> display.o: In function `setup_view':
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/display.c:1254: undefined reference to `cos'
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/display.c:1255: undefined reference to `sin'
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/display.c:1260: undefined reference to `cos'
> /home/jcebrian/parsec-3.0_gcc_47/ext/splash2/apps/radiosity/obj/amd64-linux.gcc-hooks/display.c:1261: undefined reference to `sin'
> glibps/glibps.a(glibps.o): In function `grotate_x_matrix':
> glibps.c:(.text+0x4a5): undefined reference to `sincos'
> glibps/glibps.a(glibps.o): In function `grotate_y_matrix':
> glibps.c:(.text+0x547): undefined reference to `sincos'
> glibps/glibps.a(glibps.o): In function `grotate_z_matrix':
> glibps.c:(.text+0x5e9): undefined reference to `sincos'
> glibps/glibps.a(glibps.o): In function `gnormalize_vector':
> glibps.c:(.text+0x1748): undefined reference to `sqrt'
> collect2: ld returned 1 exit status
> make: *** [radiosity] Error 1
> [PARSEC] Error: 'env version=IN_PARSEC /usr/bin/make' failed.
> 
> SOLUTION:
> 
> edit: /ext/splash2/apps/radiosity/src/makefile
> 
> -- gcc $(CFLAGS) $(LDFLAGS) $(OBJS) $(LOADLIBES) -o $(TARGET)
> 
> ++ gcc $(CFLAGS) $(OBJS) $(LOADLIBES) -o $(TARGET) $(LDFLAGS)
> 
> 
> *******************************************************************************
> 
> PROBLEM:
> 
> [PARSEC] [========== Building package splash2.volrend [2] ==========]
> [PARSEC] [---------- Analyzing package splash2.volrend ----------]
> [PARSEC] splash2.volrend depends on:  hooks
> [PARSEC] [---------- Analyzing package parsec.hooks ----------]
> [PARSEC] Package parsec.hooks already exists, proceeding.
> [PARSEC] [---------- Building package splash2.volrend ----------]
> [PARSEC] Removing old build directory.
> [PARSEC] Copying source code of package splash2.volrend.
> [PARSEC] Running 'env version=IN_PARSEC /usr/bin/make':
> m4 ../../../../null_macros/c.m4.null.pthread user_options.H > user_options.h
> ....
> gcc -c -O2 -w -DPRESHD  -Ilibtiff raytrace.c
> gcc main.o file.o option.o map.o normal.o opacity.o octree.o view.o render.o adaptive.o raytrace.o -O2 -w -DPRESHD  -Ilibtiff -o volrend -O2 -w -pthread -lm -Ilibtiff -Llibtiff -ltiff
> /usr/bin/ld: cannot find -ltiff
> collect2: ld returned 1 exit status
> make: *** [volrend] Error 1
> [PARSEC] Error: 'env version=IN_PARSEC /usr/bin/make' failed.
> 
> SOLUTION: (MANUAL SOLUTION, You should find out what is the best solution to fix this, either moving libtiff to /pkgs/libs and changing gcc.bldconf or rebuilding makefile structures)
> 
> edit: ext/splash2/apps/volrend/src/libtiff/Makefile and define BSDTYPES, for example:
> 
> CONF_LIBRARY=\
>         -DBSDTYPES \                  # <<< ADD THIS
>         -DUSE_VARARGS=0 \
>         -DUSE_PROTOTYPES=1 \
>         -DHAVE_IEEEFP=1 \
>         -DCOLORIMETRY_SUPPORT \
>         -DJPEG_SUPPORT \
>         -DYCBCR_SUPPORT \
>         -DCMYK_SUPPORT \
>         -DMMAP_SUPPORT \
>         ${NULL}
> 
> then build with make in ext/splash2/apps/volrend/src/libtiff
> 
> *******************************************************************************
> 
> PROBLEM:
> 
> [PARSEC] [========== Building package splash2x.volrend [2] ==========]
> [PARSEC] [---------- Analyzing package splash2x.volrend ----------]
> [PARSEC] splash2x.volrend depends on: parmacs hooks
> [PARSEC] [---------- Analyzing package parsec.parmacs ----------]
> [PARSEC] Package parsec.parmacs already exists, proceeding.
> [PARSEC] [---------- Analyzing package parsec.hooks ----------]
> [PARSEC] Package parsec.hooks already exists, proceeding.
> [PARSEC] [---------- Building package splash2x.volrend ----------]
> [PARSEC] Copying source code of package splash2x.volrend.
> [PARSEC] Running 'env version=pthreads /usr/bin/make':
> .........
> /home/jcebrian/extras/gcc-4.7.0/bin/gcc adaptive.o file.o main.o map.o normal.o octree.o opacity.o option.o raytrace.o render.o view.o -mavx -O2 -g -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=3.0-beta-20120904 -DENERGY_LIB -DMEASURE_FROM_START -static-libgcc -Wl,--hash-style=both,--as-needed -DENABLE_PARSEC_HOOKS -I/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/include -I/home/jcebrian/extras/likwid/include -Wall -W -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wdisabled-optimization -Wpadded -Winline -Wpointer-arith -Wsign-compare -Wendif-labels -I./libtiff -DENABLE_THREADS -pthread -o volrend -L./libtiff -L/home/jcebrian/extras/gcc-4.7.0/lib64 -L/home/jcebrian/extras/gcc-4.7.0/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/hooks/inst/amd64-linux.gcc-hooks/lib -L/home/jcebrian/parsec-3.0_gcc_47/bin/../pkgs/libs/energy_lib/lib -L/home/jcebrian/extras/likwid/lib -lm  -ltiff  -pthread -lhooks -lenergy -llikwid -lm
> /usr/bin/ld: cannot find -ltiff
> collect2: error: ld returned 1 exit status
> make: *** [volrend] Error 1
> [PARSEC] Error: 'env version=pthreads /usr/bin/make' failed.
> 
> SOLUTION: (MANUAL SOLUTION, You should find out what is the best solution to fix this, either moving libtiff to /pkgs/libs and changing gcc.bldconf or rebuilding makefile structures)
> 
> edit: ext/splash2x/apps/volrend/src/libtiff/Makefile and define BSDTYPES, for example:
> 
> CONF_LIBRARY=\
>         -DBSDTYPES \                  # <<< ADD THIS
>         -DUSE_VARARGS=0 \
>         -DUSE_PROTOTYPES=1 \
>         -DHAVE_IEEEFP=1 \
>         -DCOLORIMETRY_SUPPORT \
>         -DJPEG_SUPPORT \
>         -DYCBCR_SUPPORT \
>         -DCMYK_SUPPORT \
>         -DMMAP_SUPPORT \
>         ${NULL}
> 
> then build with make in ext/splash2x/apps/volrend/src/libtiff
> 
> 
> *******************************************************************************
> 
> #Other:
> 
> As reported before ( https://lists.cs.princeton.edu/pipermail/parsec-users/2012-September/001416.html ) , some benckmarks overwrite the gcc.bldconf CFLAGS and include O0 or -g, should this be cleaned?
> 
> i.e.,
> 
> grep -r "O0" * | grep FLAGS
> 
> pkgs/tools/cmake/src/Modules/Platform/Linux-PGI-Fortran.cmake:SET(CMAKE_Fortran_FLAGS_DEBUG_INIT "-g -O0 -Mbounds")
> pkgs/kernels/canneal/src/Makefile:CXXFLAGS+=-O0 -g
> pkgs/kernels/canneal/obj/amd64-linux.gcc-hooks/Makefile:CXXFLAGS+=-O0 -g
> pkgs/netapps/netdedup/src/client/Makefile:CFLAGS += -Wall -fno-strict-aliasing -D_XOPEN_SOURCE=600 -DENABLE_PARSEC_UPTCPIP -O0 -g
> pkgs/netapps/netdedup/src/client/Makefile:#CFLAGS += -Wall -fno-strict-aliasing -D_XOPEN_SOURCE=600  -O0 -g
> pkgs/netapps/netdedup/src/server/Makefile:CFLAGS += -O0 -g -Wall -fno-strict-aliasing -D_XOPEN_SOURCE=600
> pkgs/netapps/netdedup/obj/amd64-linux.gcc-hooks/client/Makefile:CFLAGS += -Wall -fno-strict-aliasing -D_XOPEN_SOURCE=600 -DENABLE_PARSEC_UPTCPIP -O0 -g
> pkgs/netapps/netdedup/obj/amd64-linux.gcc-hooks/client/Makefile:#CFLAGS += -Wall -fno-strict-aliasing -D_XOPEN_SOURCE=600  -O0 -g
> pkgs/netapps/netdedup/obj/amd64-linux.gcc-hooks/server/Makefile:CFLAGS += -O0 -g -Wall -fno-strict-aliasing -D_XOPEN_SOURCE=600
> pkgs/libs/tbblib/src/examples/parallel_reduce/primes/Makefile:  $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o $(PROG) $^ -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/parallel_reduce/convex_hull/Makefile:     $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o convex_hull_sample convex_hull_sample.cpp -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/parallel_reduce/convex_hull/Makefile:     $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o convex_hull_bench convex_hull_bench.cpp -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/task/tree_sum/Makefile:   $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o $(PROG) $^ -ltbbmalloc_debug -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/test_all/fibonacci/Makefile:      $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o $(PROG) $^ -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/GettingStarted/sub_string_finder/Makefile:        $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o sub_string_finder sub_string_finder.cpp -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/GettingStarted/sub_string_finder/Makefile:        $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o sub_string_finder_extended sub_string_finder_extended.cpp -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/GettingStarted/sub_string_finder/Makefile:        $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o sub_string_finder_pretty sub_string_finder_pretty.cpp -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/parallel_for/game_of_life.NET/Makefile:   $(CXX) -O0 -D_CONSOLE -g -DTBB_DO_ASSERT $(CXXFLAGS) -o $(PROG) $^ -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/parallel_for/polygon_overlay/Makefile:    $(CXX) -g -O0 -DTBB_USE_DEBUG -D_DEBUG $(CXXFLAGS) -o $(EXE) $(SRCFILES) -ltbb_debug -ltbbmalloc_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/parallel_for/seismic/Makefile:    $(CXX) -g -O0 -DTBB_USE_DEBUG $(CXXFLAGS) -o $(EXE) $< SeismicSimulation.cpp -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/parallel_for/tachyon/Makefile:MYCXXFLAGS += -O0 -g -D_DEBUG
> pkgs/libs/tbblib/src/examples/concurrent_hash_map/count_strings/Makefile:       $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o $(PROG) $^ -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/task_group/sudoku/Makefile:       $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o $(PROG) $^ -ltbb_debug $(LIBS) $(CXX0XFLAGS)
> pkgs/libs/tbblib/src/examples/pipeline/square/Makefile: $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o $(PROG) $(SQUARE) -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/examples/parallel_do/parallel_preorder/Makefile:   $(CXX) -O0 -g -DTBB_USE_DEBUG $(CXXFLAGS) -o $(PROG) $^ -ltbb_debug $(LIBS)
> pkgs/libs/tbblib/src/build/SunOS.gcc.inc:        CPLUS_FLAGS = -DTBB_USE_DEBUG -g -O0 -DUSE_PTHREAD
> pkgs/libs/tbblib/src/build/FreeBSD.gcc.inc:        CPLUS_FLAGS = -DTBB_USE_DEBUG -g -O0 -DUSE_PTHREAD
> pkgs/libs/tbblib/src/build/macos.icc.inc:    CPLUS_FLAGS = -g -O0 -DTBB_USE_DEBUG
> pkgs/libs/tbblib/src/build/macos.gcc.inc:    CPLUS_FLAGS = -g -O0 -DTBB_USE_DEBUG
> pkgs/libs/tbblib/src/build/linux.icc.inc:CPLUS_FLAGS = -O0 -g -strict_ansi -DUSE_PTHREAD -DTBB_USE_DEBUG
> pkgs/libs/tbblib/src/build/windows.gcc.inc:        CPLUS_FLAGS = -g -O0 -DTBB_USE_DEBUG
> pkgs/libs/tbblib/src/build/linux.gcc.inc:        CPLUS_FLAGS = -DTBB_USE_DEBUG -DDO_ITT_NOTIFY -g -O0 -DUSE_PTHREAD
> pkgs/libs/mesa/src/configs/beos:                CFLAGS   += -g -O0
> pkgs/libs/mesa/src/configs/beos:                CFLAGS   += -g -O0
> pkgs/libs/mesa/src/configs/beos:                CXXFLAGS += -g -O0
> pkgs/libs/mesa/src/configs/osf1:CFLAGS = -O0 -std1 -ieee_with_no_inexact -DUSE_XSHM -DPTHREADS -D_REENTRANT
> pkgs/libs/mesa/src/configs/linux-dri-debug:OPT_FLAGS  = -O0 -g
> 
> 
> 
> 
> /********************* Other data ******************************/
> 
>  *) CPU architecture:  by running "cat /proc/cpuinfo" 
>   
> 
> processor       : 0-7
> vendor_id       : GenuineIntel
> cpu family      : 6
> model           : 58
> model name      : Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
> stepping        : 9
> microcode       : 0xc
> cpu MHz         : 2200.000
> cache size      : 8192 KB
> physical id     : 0
> siblings        : 8
> core id         : 0
> cpu cores       : 4
> apicid          : 0
> initial apicid  : 0
> fpu             : yes
> fpu_exception   : yes
> cpuid level     : 13
> wp              : yes
> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
> bogomips        : 6784.67
> clflush size    : 64
> cache_alignment : 64
> address sizes   : 36 bits physical, 48 bits virtual
> power management:
> 
>  *) OS type:  by running "uname -a"
> 
> Linux 3.2.0-30-generic #48-Ubuntu SMP Fri Aug 24 16:52:48 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
> 
>  *) gcc version: by running "gcc --version"
> 
> Self-Compiled
> 
> gcc (GCC) 4.7.0
> Copyright (C) 2012 Free Software Foundation, Inc.
> 
>  *) Binutils version: by running "ld --version"
> 
> GNU ld (GNU Binutils for Ubuntu) 2.22
> Copyright 2011 Free Software Foundation, Inc.
> 
> 
> 
> 
> Jm.
> 
> 
> -- 
> ---------------------------------------------
> Juan Manuel Cebrián González
> NTNU, Trondheim, Norway
> http://www.idi.ntnu.no/people/juanmc
> http://skywalker.inf.um.es/~jcebrian/
> ---------------------------------------------
> _______________________________________________
> parsec-users mailing list
> parsec-users at lists.cs.princeton.edu
> https://lists.cs.princeton.edu/mailman/listinfo/parsec-users
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