Linux configuration

WhyIsThisAsked · June 2022

Hello, I have been using DualSPHysics in windows but now I am trying to configure it in Linux (Debian).

I can execute GenCase without problem. When I try to run DualSPhysics5.0 there is an error:

"error while loading shared libraries: libdsphchrono.so: cannot open shared object file: No such file or directory"

The file is in the folder src/lib/linux_gcc but Linux does not find it. Why? How can I solve it ?

Thank you all for your help

Zwulch · June 2022

Did you make sure to set "export dirbin=..." to the right path in your bash file?

zweihuehner · June 2022

As a workaround you can also use the binaries which are contained in the DesignSPHysics from github. The are precompiled and at least for Ubuntu 20.04 / 22.04 they work without any compilation.

So far I was not able to compile the newest versions of DualSPHysics from github in Linux. I am not sure on which environment they are compiling it, but the Installation steps in the README.txt are not working for me so I am sticking to the workaround.

imartinezestevez · June 2022

https://forums.dual.sphysics.org/discussion/2406/linux-configuration

When you launch the DualSPHysics executable make sure the path of the dynamic libraries (libdsphchrono.so & libChronoEngine.so) are in the environmental variable LD_LIBRARY_PATH. To do that, execute export LD_LIBRARY_PATH=DualSPHysics/bin/linux. Otherwise you can execute your case through a shell-script following the example provided in the folder DualSPHysics/examples/main/01_DamBreak.

imartinezestevez · June 2022

https://forums.dual.sphysics.org/discussion/comment/5405#Comment_5405

What is the error you get when you try to compile it?

zweihuehner · June 2022

https://forums.dual.sphysics.org/discussion/comment/5414#Comment_5414

Firstly I had to disable the compute_30 flag for nvcc. Otherwise it would not let me compile at all.

Then with the latest github commit I get:

[ 44%] Building NVCC (Device) object CMakeFiles/DualSPHysics5.0_linux64.dir/DualSPHysics5.0_linux64_generated_JCellDivGpuSingle_ker.cu.o
nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/usr/include/c++/11/bits/std_function.h:435:145: error: parameter packs not expanded with ‘...’:
 435 |        function(_Functor&& __f)
     |                                                                                                                                                ^ 
/usr/include/c++/11/bits/std_function.h:435:145: note:        ‘_ArgTypes’
/usr/include/c++/11/bits/std_function.h:530:146: error: parameter packs not expanded with ‘...’:
 530 |        operator=(_Functor&& __f)
     |                                                                                                                                                 ^ 
/usr/include/c++/11/bits/std_function.h:530:146: note:        ‘_ArgTypes’
CMake Error at DualSPHysics5.0_linux64_generated_JCellDivGpuSingle_ker.cu.o.cmake:280 (message):
 Error generating file
 /home/fafs/Dev/DualSPHysics/src/source/build/CMakeFiles/DualSPHysics5.0_linux64.dir//./DualSPHysics5.0_linux64_generated_JCellDivGpuSingle_ker.cu.o

I have:

Ubuntu 22.04
Cuda 11.5
gcc 11.2

Kind regards,

Faro

imartinezestevez · June 2022

Hello @zweihuehner , the problem is that Cuda 11.5 is not allowed to compile the code yet. Yo have to use Cuda 9.2

Regards

Myiced · July 2022

https://forums.dual.sphysics.org/discussion/comment/5418#Comment_5418

Hello, I just compile v5.0 with cuda11.7, It's not difficult. Just modify Makefile and match your GPU with Cuda arch . I recommend referring this website https://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards/

circles · August 2022

https://forums.dual.sphysics.org/discussion/comment/5422#Comment_5422

Hello, I am trying to run the latest release on HPC clusters. GenCase runs without a problem, DualSPHysics throws an error saying caseName_out is unrecognized or invalid.

*** Exception (JCfgRun::ErrorParm)
Text: Parameter "caseName_out" unrecognised or invalid. (Level cfg:0, Parameter:3)

Following this post, I did modify the Makefile to make sure that the cuda version and compute capability match with the the one on the cluster, I then built the executables; however, I keep getting the same error.

I saw couple of similar posts on this forum, but most of them seems to remain unanswered. I was hoping maybe someone knows how to fix it.

Thanks!

circles · August 2022

In my .sh file I modified the dualsphysicsgpu line as follows

${dualsphysicsgpu} -gpu :0 -dirout ${dirout}/${name} -name ${dirout} -dirdataout data -svres

After which, the Cuda device was successfully identified but then it throws another error which says

*** Exception (JSphGpuSingle::LoadCaseConfig) at JSph.cpp:920
Text: Case configuration was not found.
File: case_out.xml

I am not sure why it is doing this when I already can see the .xml file in the case_out folder.

circles · August 2022

I had to change the line

${dualsphysicsgpu} -gpu :0 -dirout ${dirout}/${name} -name ${dirout} -dirdataout data -svres

to

${dualsphysicsgpu} -gpu :0 -name${dirout}/${name} -dirout ${dirout} -dirdataout data -svres

It seems to be working right now.

Myiced · August 2022

https://forums.dual.sphysics.org/discussion/comment/5480#Comment_5480

Forgive me for not replying in time，congratulations🙂

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Notice	rich is deprecated. Use FormatService::renderHtml($content, Formats\RichFormat::FORMAT_KEY) instead. #0 [internal function]: gdn_ErrorHandler(16384, 'rich is depreca...', '/var/www/forums...', 950, Array) #1 /var/www/forums-dual-sphysics-org/library/core/functions.general.php(950): trigger_error('rich is depreca...', 16384) #2 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1729): deprecated('rich', 'FormatService::...') #3 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1479): Gdn_Format::rich('[{"insert":"Hel...') #4 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(24): Gdn_Format::to('[{"insert":"Hel...', 'Rich') #5 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(170): formatBody(Object(stdClass)) #6 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/comments.php(19): writeComment(Object(stdClass), Object(DiscussionController), Object(Gdn_Session), 6) #7 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/index.php(53): include('/var/www/forums...') #8 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(778): include('/var/www/forums...') #9 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(1382): Gdn_Controller->fetchView('', false, false) #10 /var/www/forums-dual-sphysics-org/library/core/class.pluggable.php(217): Gdn_Controller->xRender() #11 /var/www/forums-dual-sphysics-org/applications/vanilla/controllers/class.discussioncontroller.php(310): Gdn_Pluggable->__call('render', Array) #12 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(862): DiscussionController->index('2406', 'linux-configura...', '') #13 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(279): Gdn_Dispatcher->dispatchController(Object(Gdn_Request), Array) #14 /var/www/forums-dual-sphysics-org/index.php(29): Gdn_Dispatcher->dispatch() #15 {main}
Notice	rich is deprecated. Use FormatService::renderHtml($content, Formats\RichFormat::FORMAT_KEY) instead. #0 [internal function]: gdn_ErrorHandler(16384, 'rich is depreca...', '/var/www/forums...', 950, Array) #1 /var/www/forums-dual-sphysics-org/library/core/functions.general.php(950): trigger_error('rich is depreca...', 16384) #2 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1729): deprecated('rich', 'FormatService::...') #3 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1479): Gdn_Format::rich('[{"insert":"\\n"...') #4 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(24): Gdn_Format::to('[{"insert":"\\n"...', 'Rich') #5 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(170): formatBody(Object(stdClass)) #6 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/comments.php(19): writeComment(Object(stdClass), Object(DiscussionController), Object(Gdn_Session), 7) #7 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/index.php(53): include('/var/www/forums...') #8 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(778): include('/var/www/forums...') #9 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(1382): Gdn_Controller->fetchView('', false, false) #10 /var/www/forums-dual-sphysics-org/library/core/class.pluggable.php(217): Gdn_Controller->xRender() #11 /var/www/forums-dual-sphysics-org/applications/vanilla/controllers/class.discussioncontroller.php(310): Gdn_Pluggable->__call('render', Array) #12 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(862): DiscussionController->index('2406', 'linux-configura...', '') #13 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(279): Gdn_Dispatcher->dispatchController(Object(Gdn_Request), Array) #14 /var/www/forums-dual-sphysics-org/index.php(29): Gdn_Dispatcher->dispatch() #15 {main}
Notice	rich is deprecated. Use FormatService::renderHtml($content, Formats\RichFormat::FORMAT_KEY) instead. #0 [internal function]: gdn_ErrorHandler(16384, 'rich is depreca...', '/var/www/forums...', 950, Array) #1 /var/www/forums-dual-sphysics-org/library/core/functions.general.php(950): trigger_error('rich is depreca...', 16384) #2 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1729): deprecated('rich', 'FormatService::...') #3 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1479): Gdn_Format::rich('[{"insert":{"em...') #4 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(24): Gdn_Format::to('[{"insert":{"em...', 'Rich') #5 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(170): formatBody(Object(stdClass)) #6 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/comments.php(19): writeComment(Object(stdClass), Object(DiscussionController), Object(Gdn_Session), 8) #7 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/index.php(53): include('/var/www/forums...') #8 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(778): include('/var/www/forums...') #9 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(1382): Gdn_Controller->fetchView('', false, false) #10 /var/www/forums-dual-sphysics-org/library/core/class.pluggable.php(217): Gdn_Controller->xRender() #11 /var/www/forums-dual-sphysics-org/applications/vanilla/controllers/class.discussioncontroller.php(310): Gdn_Pluggable->__call('render', Array) #12 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(862): DiscussionController->index('2406', 'linux-configura...', '') #13 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(279): Gdn_Dispatcher->dispatchController(Object(Gdn_Request), Array) #14 /var/www/forums-dual-sphysics-org/index.php(29): Gdn_Dispatcher->dispatch() #15 {main}
Notice	rich is deprecated. Use FormatService::renderHtml($content, Formats\RichFormat::FORMAT_KEY) instead. #0 [internal function]: gdn_ErrorHandler(16384, 'rich is depreca...', '/var/www/forums...', 950, Array) #1 /var/www/forums-dual-sphysics-org/library/core/functions.general.php(950): trigger_error('rich is depreca...', 16384) #2 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1729): deprecated('rich', 'FormatService::...') #3 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1479): Gdn_Format::rich('[{"insert":"In ...') #4 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(24): Gdn_Format::to('[{"insert":"In ...', 'Rich') #5 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(170): formatBody(Object(stdClass)) #6 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/comments.php(19): writeComment(Object(stdClass), Object(DiscussionController), Object(Gdn_Session), 9) #7 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/index.php(53): include('/var/www/forums...') #8 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(778): include('/var/www/forums...') #9 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(1382): Gdn_Controller->fetchView('', false, false) #10 /var/www/forums-dual-sphysics-org/library/core/class.pluggable.php(217): Gdn_Controller->xRender() #11 /var/www/forums-dual-sphysics-org/applications/vanilla/controllers/class.discussioncontroller.php(310): Gdn_Pluggable->__call('render', Array) #12 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(862): DiscussionController->index('2406', 'linux-configura...', '') #13 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(279): Gdn_Dispatcher->dispatchController(Object(Gdn_Request), Array) #14 /var/www/forums-dual-sphysics-org/index.php(29): Gdn_Dispatcher->dispatch() #15 {main}
Notice	rich is deprecated. Use FormatService::renderHtml($content, Formats\RichFormat::FORMAT_KEY) instead. #0 [internal function]: gdn_ErrorHandler(16384, 'rich is depreca...', '/var/www/forums...', 950, Array) #1 /var/www/forums-dual-sphysics-org/library/core/functions.general.php(950): trigger_error('rich is depreca...', 16384) #2 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1729): deprecated('rich', 'FormatService::...') #3 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1479): Gdn_Format::rich('[{"insert":"I h...') #4 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(24): Gdn_Format::to('[{"insert":"I h...', 'Rich') #5 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(170): formatBody(Object(stdClass)) #6 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/comments.php(19): writeComment(Object(stdClass), Object(DiscussionController), Object(Gdn_Session), 10) #7 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/index.php(53): include('/var/www/forums...') #8 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(778): include('/var/www/forums...') #9 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(1382): Gdn_Controller->fetchView('', false, false) #10 /var/www/forums-dual-sphysics-org/library/core/class.pluggable.php(217): Gdn_Controller->xRender() #11 /var/www/forums-dual-sphysics-org/applications/vanilla/controllers/class.discussioncontroller.php(310): Gdn_Pluggable->__call('render', Array) #12 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(862): DiscussionController->index('2406', 'linux-configura...', '') #13 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(279): Gdn_Dispatcher->dispatchController(Object(Gdn_Request), Array) #14 /var/www/forums-dual-sphysics-org/index.php(29): Gdn_Dispatcher->dispatch() #15 {main}
Notice	rich is deprecated. Use FormatService::renderHtml($content, Formats\RichFormat::FORMAT_KEY) instead. #0 [internal function]: gdn_ErrorHandler(16384, 'rich is depreca...', '/var/www/forums...', 950, Array) #1 /var/www/forums-dual-sphysics-org/library/core/functions.general.php(950): trigger_error('rich is depreca...', 16384) #2 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1729): deprecated('rich', 'FormatService::...') #3 /var/www/forums-dual-sphysics-org/library/core/class.format.php(1479): Gdn_Format::rich('[{"insert":{"em...') #4 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(24): Gdn_Format::to('[{"insert":{"em...', 'Rich') #5 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/helper_functions.php(170): formatBody(Object(stdClass)) #6 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/comments.php(19): writeComment(Object(stdClass), Object(DiscussionController), Object(Gdn_Session), 11) #7 /var/www/forums-dual-sphysics-org/applications/vanilla/views/discussion/index.php(53): include('/var/www/forums...') #8 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(778): include('/var/www/forums...') #9 /var/www/forums-dual-sphysics-org/library/core/class.controller.php(1382): Gdn_Controller->fetchView('', false, false) #10 /var/www/forums-dual-sphysics-org/library/core/class.pluggable.php(217): Gdn_Controller->xRender() #11 /var/www/forums-dual-sphysics-org/applications/vanilla/controllers/class.discussioncontroller.php(310): Gdn_Pluggable->__call('render', Array) #12 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(862): DiscussionController->index('2406', 'linux-configura...', '') #13 /var/www/forums-dual-sphysics-org/library/core/class.dispatcher.php(279): Gdn_Dispatcher->dispatchController(Object(Gdn_Request), Array) #14 /var/www/forums-dual-sphysics-org/index.php(29): Gdn_Dispatcher->dispatch() #15 {main}

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