[SOLVED] Error configure SOFA in cmake-gui about lpthreads

[adrien]

Hello everyone,

I’m trying to build SOFA.
The first step, the configuration with cmake-gui, encounters an error with -lpthreads and therefore the configuration cannot be completed. Here is the CMakeError.log content :

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_22e98/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_22e98.dir/build.make CMakeFiles/cmTC_22e98.dir/build
gmake[1] : on entre dans le répertoire « /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp »
Building C object CMakeFiles/cmTC_22e98.dir/CheckFunctionExists.c.o
/usr/bin/clang   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_22e98.dir/CheckFunctionExists.c.o   -c /usr/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTC_22e98
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_22e98.dir/link.txt --verbose=1
/usr/bin/clang  -DCHECK_FUNCTION_EXISTS=pthread_create    -rdynamic CMakeFiles/cmTC_22e98.dir/CheckFunctionExists.c.o  -o cmTC_22e98 -lpthreads 
/usr/bin/ld : ne peut trouver -lpthreads
clang-6.0: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [CMakeFiles/cmTC_22e98.dir/build.make:87: cmTC_22e98] Error 1
gmake[1] : on quitte le répertoire « /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp »
gmake: *** [Makefile:126: cmTC_22e98/fast] Error 2

I tried to configure with clang and cc and each time the same error.

I’m working on Fedora 28 64-bit.

Thanks in advance for your help

[Guillaume]

Hi,

Did you install all SOFA dependencies? Unfortunately, our documentation is Ubuntu oriented but equivalences can be found easily.
I’d go for the Fedora equivalent of build-essential: dnf install @development-tools

source: https://unix.stackexchange.com/questions/1338/what-is-the-fedora-equivalent-of-the-debian-build-essential-package

Hope that helps,
Guillaume.

[adrien]

Hello Guillaume,

Thanks for your answer. I just tried what you adviced. Here is the Konsole output:

[stage@port_poire usr]$ sudo dnf install @development-tools
[sudo] Mot de passe de stage : 
Dernière vérification de l’expiration des métadonnées effectuée il y a 2:20:41 le ven. 18 mai 2018 15:49:34 CEST.
Le groupe « Outils de développement » est déjà installé.
Dépendances résolues.
Rien à faire.
Terminé !

It seems that it is not the problem.

[adrien]

Hi,

I found a post where mentioned the libpthread file:link
So I checked and found libpthread_nonshared.a which is a library for parallel execution model. It seems to be the dependency that I need to compile SOFA. Therefore, I installed glibc and I checked again the libpthread lib but I didn’t find it.

Do you know if the lipthread is a known problem ? Would you have an idea to solve it ?

[adrien]

sorry here is the link:

https://www.centos.org/forums/viewtopic.php?t=3517

[Guillaume]

Hi,

No, never encountered this error before.
This thread may help.
Perhaps @jnbrunet could help, he knows Fedora well 🙂

[Hugo]

hey @adrien

did you take the time to look at Guillaume’s link? I am pretty sure clues in this thread may help you in solving you config problem. Are you able to find pthread somewhere on your system?

[adrien]

Hello Hugo,

Yes I looked at the links.
The lib libpthread is installed on my system under /usr/lib64/.
I just tried to check if the function pthread is the file /usr/lib64/libpthread.so.0 and I obtained nm: /usr/lib64/libpthread.so.0: aucun symbole which means that the function isn’t in the file.

Could the version of the lib be the bug ?

Thanks for your help

[adrien]

Hello,

I tried to install older version of glibc (2.15) to change the libpthread version and when I run configure sudo ../glibc-2.15/configure --prefix=/usr --disable-profile --enable-add-ons --enable-kernel=2.6.25 --libexecdir=/usr/lib/glibc
I obtained

*** These critical programs are missing or too old: gcc make
*** Check the INSTALL file for required versions.

witch version of glibc should I install?

Thanks

[Hugo]

Hi @adrien,

I don’t see in your above posts any reference to the link we sent you.
Have you checked Edit 1, 2 and 3 ?

find /lib -name "*pthread*"

then test:

nm /lib/x86_64-linux-gnu/libpthread.so.0 | grep "pthread_create"

Use a minimal CMakeLists.txt to test:

cmake_minimum_required (VERSION 2.8.7)
find_package(Threads)

Check whether there is any version mismatch.
Best,

Hugo

[adrien]

Hi Hugo,

I did it and I obtained nm: /usr/lib64/libpthread.so.0: aucun symbole to test if pethread_create exists and I ran the CMakeLists.txt and it gave:

-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE 

Thanks for your help

[Hugo]

What about the first command: find /lib -name "*pthread*" ?

[adrien]

I used locate libpthread to found the file libpthread.so.0 and when I used find /lib -name "*pthread*" it found nothing.
It seems that the lib is installed in /usr/lib64/ on my system and not in /lib/ but even in the /usr/lib64/ there isn’t the function pthread-create which raised the cmake error.

[jnbrunet]

Hello,

I’m not sure about fedora 28, but with fedora 27 I have:

$ ldd bin/runSofa | grep -i pthread
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff9c41fb000)

$ rpm -qf /lib64/libpthread.so.0
glibc-2.26-28.fc27.x86_64

And

$ namei /lib64/libpthread.so.0
f: /lib64/libpthread.so.0
 d /
 l lib64 -> usr/lib64
   d usr
   d lib64
 l libpthread.so.0 -> libpthread-2.26.so
   - libpthread-2.26.so

Which means my /lib64/libpthread.so.0 was imported by the glib-2.26 package. I find it very strange that nm didn’t found any symbol in your libpthread.so.0 file. Maybe try to reinstall the glib package?

[adrien]

Hello Jean-Nicolas,

I reinstalled the glib package as you adviced me and now I found:

[stage@port_poire ~]$ nm /lib64/libpthread.so.0 | grep "pthread_create"
0000000000007870 t __pthread_create_2_1
0000000000005bee t __pthread_create_2_1.cold.12
0000000000007870 T pthread_create@@GLIBC_2.2.5

Nevertheless I have again the same configuration error (CMakeError.log):

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_22e98/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_22e98.dir/build.make CMakeFiles/cmTC_22e98.dir/build
gmake[1] : on entre dans le répertoire « /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp »
Building C object CMakeFiles/cmTC_22e98.dir/CheckFunctionExists.c.o
/usr/bin/clang   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_22e98.dir/CheckFunctionExists.c.o   -c /usr/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTC_22e98
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_22e98.dir/link.txt --verbose=1
/usr/bin/clang  -DCHECK_FUNCTION_EXISTS=pthread_create    -rdynamic CMakeFiles/cmTC_22e98.dir/CheckFunctionExists.c.o  -o cmTC_22e98 -lpthreads 
/usr/bin/ld : ne peut trouver -lpthreads
clang-6.0: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [CMakeFiles/cmTC_22e98.dir/build.make:87: cmTC_22e98] Error 1
gmake[1] : on quitte le répertoire « /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp »
gmake: *** [Makefile:126: cmTC_22e98/fast] Error 2

Could the clang package play a role in that problem ?

Thanks for your help.

[jnbrunet]

Maybe, can you give me the output of the following commands:

1. /usr/bin/clang --version
2. /usr/bin/ld --verbose | grep SEARCH
3. CURDIR=$PWD; cd /tmp && cp /usr/share/cmake/Modules/CheckFunctionExists.c . && /usr/bin/clang -DCHECK_FUNCTION_EXISTS=pthread_create -o CheckFunctionExists.c.o -c CheckFunctionExists.c && /usr/bin/clang -DCHECK_FUNCTION_EXISTS=pthread_create -rdynamic CheckFunctionExists.c.o -o CheckFunctionExists -lpthread -v; rm CheckFunctionExists*; cd $CURDIR

Edit:
Also, the output of
4. ll /usr/lib64 | grep -i pthread

[adrien]

yes, of course:

[stage@port_poire ~]$ /usr/bin/clang --version
clang version 6.0.0 (tags/RELEASE_600/final)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

[stage@port_poire ~]$ /usr/bin/ld --verbose | grep SEARCH
SEARCH_DIR("=/usr/x86_64-redhat-linux/lib64"); SEARCH_DIR("=/usr/lib64"); SEARCH_DIR("=/usr/local/lib64"); SEARCH_DIR("=/lib64"); SEARCH_DIR("=/usr/x86_64-redhat-linux/lib"); SEARCH_DIR("=/usr/local/lib"); SEARCH_DIR("=/lib"); SEARCH_DIR("=/usr/lib");

[stage@port_poire ~]$ CURDIR=$PWD; cd /tmp && cp /usr/share/cmake/Modules/CheckFunctionExists.c . && /usr/bin/clang -DCHECK_FUNCTION_EXISTS=pthread_create -o CheckFunctionExists.c.o -c CheckFunctionExists.c && /usr/bin/clang -DCHECK_FUNCTION_EXISTS=pthread_create -rdynamic CheckFunctionExists.c.o -o CheckFunctionExists -lpthread -v; rm CheckFunctionExists*; cd $CURDIR
clang version 6.0.0 (tags/RELEASE_600/final)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
Found candidate GCC installation: /usr/bin/../lib/gcc/x86_64-redhat-linux/8
Found candidate GCC installation: /usr/lib/gcc/x86_64-redhat-linux/8
Selected GCC installation: /usr/bin/../lib/gcc/x86_64-redhat-linux/8
Candidate multilib: .;@m64
Candidate multilib: 32;@m32
Selected multilib: .;@m64
 "/usr/bin/ld" -export-dynamic --hash-style=gnu --no-add-needed --build-id --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o CheckFunctionExists /usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64/crt1.o /usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64/crti.o /usr/bin/../lib/gcc/x86_64-redhat-linux/8/crtbegin.o -L/usr/bin/../lib/gcc/x86_64-redhat-linux/8 -L/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64 -L/usr/bin/../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../.. -L/usr/bin/../lib -L/lib -L/usr/lib CheckFunctionExists.c.o -lpthread -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/bin/../lib/gcc/x86_64-redhat-linux/8/crtend.o /usr/bin/../lib/gcc/x86_64-redhat-linux/8/../../../../lib64/crtn.o

[jnbrunet]

Also, the output of

ll /usr/lib64 | grep -i pthread

[adrien]

[stage@port_poire ~]$ ll /usr/lib64 | grep -i pthread
lrwxrwxrwx.  1 root root        30 15 févr. 17:28 libevent_pthreads-2.1.so.6 -> libevent_pthreads-2.1.so.6.0.2
-rwxr-xr-x.  1 root root     11416 15 févr. 17:28 libevent_pthreads-2.1.so.6.0.2
lrwxrwxrwx.  1 root root        27  8 févr. 03:53 libgpgme++-pthread.so.2 -> libgpgme++-pthread.so.2.8.0
-rwxr-xr-x.  1 root root    354104  8 févr. 03:54 libgpgme++-pthread.so.2.8.0
lrwxrwxrwx.  1 root root        37  8 févr. 11:00 liblttng-ust-pthread-wrapper.so.0 -> liblttng-ust-pthread-wrapper.so.0.0.0
-rwxr-xr-x.  1 root root     24824  8 févr. 11:00 liblttng-ust-pthread-wrapper.so.0.0.0
-rwxr-xr-x.  1 root root    154128 24 mai   17:38 libpthread-2.27.so
-rw-r--r--.  1 root root    164048 24 mai   17:38 libpthread.a
-rw-r--r--.  1 root root      1724 24 mai   17:38 libpthread_nonshared.a
-rw-r--r--.  1 root root       222 24 mai   17:36 libpthread.so
lrwxrwxrwx.  1 root root        18 24 mai   17:36 libpthread.so.0 -> libpthread-2.27.so
lrwxrwxrwx.  1 root root        25 10 mars   2017 libpthread-stubs.so.0 -> libpthread-stubs.so.0.0.0
-rwxr-xr-x.  1 root root      6768 10 mars   2017 libpthread-stubs.so.0.0.0

[jnbrunet]

Not sure where you got those libpthread stubs files and the static static library.

Did you installed glibc-devel package?

Can you give me the output of
1. rpm -qf /usr/lib64/libpthread-stubs.so.0
2. rpm -qf /usr/lib64/libpthread.a
3. cat /usr/lib64/libpthread.so

[adrien]

I installed glibc-static package and glibc-devel package was already installed
1. `[stage@port_poire ~]$ rpm -qf /usr/lib64/libpthread-stubs.so.0
libpthread-stubs-0.2-5.2.x86_64`

2. `[stage@port_poire ~]$ rpm -qf /usr/lib64/libpthread.a
glibc-static-2.27-15.fc28.x86_64`

3. `[stage@port_poire ~]$ cat /usr/lib64/libpthread.so
/* GNU ld script
Use the shared library, but some functions are only in
the static library, so try that secondarily. */
OUTPUT_FORMAT(elf64-x86-64)
GROUP ( /lib64/libpthread.so.0 /usr/lib64/libpthread_nonshared.a )`

[jnbrunet]

Then I’m not really sure where your problem comes from. From your results, everything seems fine, you even linked the same test program from cmake without the linked error…

The only difference I have with you is that I don’t have that static package installed, but this should not make a difference since the linker should use the dynamic library by default, unless you manually imposed static linking, which I don’t even think it’s possible with sofa.

Can you try again the compilation with an empty build directory of sofa? Try to put the least cmake options as possible (plugins, etc). Maybe add the -DCMAKE_VERBOSE_MAKEFILE=ON to the cmake command to get more hints.

[adrien]

I tried the compilation with an empty build directory and with any options for cmake and it seems that nothing has changed.

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_2accb/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_2accb.dir/build.make CMakeFiles/cmTC_2accb.dir/build
gmake[1] : on entre dans le répertoire « /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp »
Building C object CMakeFiles/cmTC_2accb.dir/CheckFunctionExists.c.o
/usr/bin/clang   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_2accb.dir/CheckFunctionExists.c.o   -c /usr/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTC_2accb
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2accb.dir/link.txt --verbose=1
/usr/bin/clang  -DCHECK_FUNCTION_EXISTS=pthread_create    -rdynamic CMakeFiles/cmTC_2accb.dir/CheckFunctionExists.c.o  -o cmTC_2accb -lpthreads 
/usr/bin/ld : ne peut trouver -lpthreads
clang-6.0: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [CMakeFiles/cmTC_2accb.dir/build.make:87: cmTC_2accb] Error 1
gmake[1] : on quitte le répertoire « /home/stage/Documents/Adrien/sofa/build/build-v17.12/CMakeFiles/CMakeTmp »
gmake: *** [Makefile:126: cmTC_2accb/fast] Error 2

[jnbrunet]

Well, I’ve just tested with a clean fedora 28 vm. I saved the exact commands used from the freshly installed OS to the compilation of Sofa:

1. $ sudo dnf update -y
2. $ sudo dnf install -y gcc-c++ clang cmake cmake-gui git qt5-devel boost-devel python2-devel libpng-devel libjpeg-turbo-devel libtiff-devel zlib-devel glew-devel
3. $ git clone https://github.com/sofa-framework/sofa.git
4. $ cd sofa
5. $ mkdir build
6. $ cd build
7. $ cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
8. $ make

I’ve compiled successfully with both v17.12 and master branches. I’ve also tried with glibc-static and glibc-devel to see if there is a confusion in the dependencies, and everything built fine. Here is the versions of the tool installed:

cmake: 3.11.2
clang: 6.0.0
glibc: 2.27

Maybe you could try reinstall the cmake and clang packages… Make sure that you only use the tools from the fedora repositories, and not the ones you compiled yourself.

[adrien]

I used your command line
$ sudo dnf install -y gcc-c++ clang cmake cmake-gui git qt5-devel boost-devel python2-devel libpng-devel libjpeg-turbo-devel libtiff-devel zlib-devel glew-devel
it installed the package qt5-devel ( I already installed qt thanks to the link that is given in SOFA documentation) then the cmake configuration worked.

Thanks that helped me.

However, there is still an error when I tried to compile with ninja or make (after generation of Makefile) :

/home/stage/Documents/Adrien/sofa/src/SofaGeneral/../modules/SofaBoundaryCondition/FixedPlaneConstraint.inl:173:31:   requis par « void sofa::component::projectiveconstraintset::FixedPlaneConstraint<DataTypes>::projectResponse(const sofa::core::MechanicalParams*, sofa::component::projectiveconstraintset::FixedPlaneConstraint<DataTypes>::DataVecDeriv&) [avec DataTypes = sofa::defaulttype::StdRigidTypes<3, double>; sofa::component::projectiveconstraintset::FixedPlaneConstraint<DataTypes>::DataVecDeriv = sofa::core::objectmodel::Data<sofa::helper::vector<sofa::defaulttype::RigidDeriv<3, double>, sofa::helper::CPUMemoryManager<sofa::defaulttype::RigidDeriv<3, double> > > >; typename DataTypes::VecDeriv = sofa::helper::vector<sofa::defaulttype::RigidDeriv<3, double>, sofa::helper::CPUMemoryManager<sofa::defaulttype::RigidDeriv<3, double> > >] »
/home/stage/Documents/Adrien/sofa/src/modules/SofaBoundaryCondition/FixedPlaneConstraint.cpp:58:44:   requis depuis ici
/home/stage/Documents/Adrien/sofa/src/modules/SofaBoundaryCondition/FixedPlaneConstraint.cpp:74:100: erreur interne du compilateur: dans type_dependent_expression_p, à cp/pt.c:25100
    for (helper::vector< unsigned int > ::const_iterator it = this->indices.getValue().begin(); it != this->indices.getValue().end(); ++it)
                                                                                                ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Veuillez soumettre un rapport d’anomalies complet,
avec la sortie du préprocesseur si nécessaire.
Voir <http://bugzilla.redhat.com/bugzilla> pour les instructions.
La source convertie par le préprocesseur a été stockée dans le fichier /tmp/ccVMjYoh.out, veuillez l'attacher à votre rapport d'anomalie.
make[2]: *** [SofaGeneral/SofaBoundaryCondition/CMakeFiles/SofaBoundaryCondition.dir/build.make:167: SofaGeneral/SofaBoundaryCondition/CMakeFiles/SofaBoundaryCondition.dir/FixedPlaneConstraint.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:3112: SofaGeneral/SofaBoundaryCondition/CMakeFiles/SofaBoundaryCondition.dir/all] Error 2
make: *** [Makefile:163: all] Error 2

I don’t understand what it means precisely. Do you have an idea about it ?

[Author]

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