[parsec-users] The Beta Release of PARSEC 3.0

Juan Manuel Cebrián González juanmc at idi.ntnu.no
Tue Sep 18 10:59:05 EDT 2012


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/
---------------------------------------------
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