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Dear René,
Thanks for such a prompt reply. The log files, I sent were from the
release-0.1.2 branch. However, I did try "master" as well, but the error
remains same.
$PICSRC/configure ~/paramSets/case001
in release-0.1.2 branch as well as master branch gives following error:-
CMake Error at CMakeLists.txt:38 (add_subdirectory):
The binary directory
/home/ajitup/build/build_picongpu
is already used to build a source directory. It cannot be used to build
source directory
/home/ajitup/code.PIConGPU/picongpu-master/src/picongpu
Specify a unique binary directory name.
CMake Error at CMakeLists.txt:38 (add_subdirectory):
The binary directory
/home/ajitup/build/build_picongpu
is already used to build a source directory. It cannot be used to build
source directory
/home/ajitup/code.PIConGPU/picongpu-master/src/picongpu
Specify a unique binary directory name.
Whereas, there is no quota set by HPC system and I am able to write/create
a file/folder in ~/build directory. my PICSRC is ~/src/picongpu and I
build the code in ~/build directory. Further error is in CMakeError.log :
Determining if the pthread_create exist failed with the following output:
Change Dir: /home/ajitup/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_d035f/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_d035f.dir/build.make
CMakeFiles/cmTC_d035f.dir/build
gmake[1]: Entering directory '/home/ajitup/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_d035f.dir/CheckSymbolExists.c.o
/usr/bin/cc -fPIC -o CMakeFiles/cmTC_d035f.dir/CheckSymbolExists.c.o
-c /home/ajitup/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTC_d035f
/usr/local/bin/cmake -E cmake_link_script
CMakeFiles/cmTC_d035f.dir/link.txt --verbose=1
/usr/bin/cc -fPIC CMakeFiles/cmTC_d035f.dir/CheckSymbolExists.c.o -o
cmTC_d035f -rdynamic
CMakeFiles/cmTC_d035f.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0x1b): undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_d035f.dir/build.make:97: recipe for target 'cmTC_d035f'
failed
gmake[1]: *** [cmTC_d035f] Error 1
gmake[1]: Leaving directory '/home/ajitup/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_d035f/fast' failed
gmake: *** [cmTC_d035f/fast] Error 2
File /home/ajitup/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include <pthread.h>
int main(int argc, char** argv)
{
(void)argv;
#ifndef pthread_create
return ((int*)(&pthread_create))[argc];
#else
(void)argc;
return 0;
#endif
}
I have attached some test files which I compiled to check for
pthread_create function using $cc -lpthread ***.c -o ***.out
and they compiled. A search for libpthread shows it in /lib as well as
/lib64 in system-root. I have gcc 4.8.5, and cuda 7.5. I did try dev
branch, but as you suggested it will require enabling c++11 support. The
error in dev branch is:
Please enable C++11 with `-std=c++11` or `-DCMAKE_CXX_STANDARD=11` when
compiling with nvcc 7.5
I will try adding c++11 support and let you know, but the CMakeError.log
shows lpthread issue even in dev branch.
regards,
ajit
Attachements: Cmake log files for release-branch
test codes for lpthread
CMakeLists.txt from release-0.1.2
> ---------------------------- Original Message ----------------------------
> Subject: Re: Help on PIConGPU?
> From: René Widera <r.widera@hzdr.de>
> Date: Wed, April 27, 2016 2:14 pm
> To: "Dr. Ajit Upadhyay" <ajitup@rrcat.gov.in>
> ------------------------------------------------------------------
> Dear Dr. Ajit Upadhyay,
>
> thank you for participate our project PIConGPU.
>
> Please subscribe at our mailing list [1] for future issues with
> picongpu. The mailing list helps the community if other run in equal
> issues.
>
> Currently I have only looked very fast to your problem, I will take a
> deeper analysis tomorrow.
> Which version of PIConGPU you used? master or dev
> For cuda 7.5 please switch to `dev` because as I remember we need to
> enable C++11 for cuda 7.5 else PIConGPU will not compile and the master
> is not C++11 compatible.
> Please keep in mind that the branch `dev` is our working branch and
> interfaces can be changed.
> There will be a new release in one or two weeks available.
>
> I looked first at your file `build_output_shell` and found the error
> ```
> CMake Error at CMakeLists.txt:38 (add_subdirectory):
> The binary directory
> /home/ajitup/build/build_picongpu
> ```
> This looks like you are not allowed to create directories in `~/build`.
> Maybe your HPC System set a quota for your home directory which results
> in the case that no new files can be created. Could you please check
> this behavior.
>
> pthread issue:
>
> Could you please provide me with the cmake script and all needed files.
> It looks like the linker flag `lpthread` is missing in your example.
>
> If some of the issues are solved till tomorrow please give me a feedback.
>
> btw: please skip the `Dr.` before my name but I would be glad to get a
> honorary degree ;-)
>
> best regards,
> René
>
> [1]
> https://github.com/ComputationalRadiationPhysics/picongpu/tree/dev#users
>
> On 27.04.2016 09:43, Dr. Ajit Upadhyay wrote:
>> Dear Dr. René Widera,
>>
>> I downloaded the release-0.1.2 branch of code and tried to compile it
on a HP Z840 (Intel Xeon E5-2630v3 2.4 1866 8C x 2, 128GB memory)
workstation with two Nividia Quadro 4200 GPUs (compatible with CUDA).
The OS on my workstation is openSuSe Leap 42.1 with cuda-7.5. I have
tested some examples from the nvidia-cuda library and they are working
fine.
>>
>> I have compiled all the libraries required by PIConGPU successfully and
placed them as per the instructions in /picongpu/src/install.md file.
However, when I try to compile the code itself, it gives a strange
error> of pthread_create function (please look at the attached
CMakeError.log).
>>
>> I did check that the relevant library is in its place
>> (/lib/libpthread-2.19.so, glibc-2.19-19.1_x86_64). I did google for the
error but could not resolve this issue as the problem seems to be with
"configure" script of the picongpu code.
>>
>> I made a test program from CMakeError.log file and compiled it
separately and it compiles (please have a look at pthread_check_log, a
few lines of code are listed and it compiles all these which uses this
function). I have attached the output dumped on the linux-terminal in
file build_output_shell. Other files created by cmake are also
attached.
>>
>> Could you please point out where is the fault in my setup of this code
>> or what should I do to run this code.
>>
>> Regards,
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