Re: [deal.II] deal.ii Installation : expand_instantiations Error
Hi all y'all
I am the consultant helping Aaditya compile deal.II on NERSC's Cori system.
Let me start by trying to address Wolfgang's questions:
> that would help, but the question is why that is necessary
Good question! I've never had to do this myself (the cray compiler wrappers
usually take care of things like this). I had a look around -- and a chat
with some of my colleagues -- and our working theory is that:
1) the cmake script is interfering with the cray compiler wrappers
2) the cmake script is adding libraries that it's detecting in the
environment
> What does this library do
AtpSigHandler is part of Cray's ATP support -- Abnormal Termination
Processing (ATP) is a system that monitors Cray system user applications.
(taken from `man atp_intro`)
> If this kind of change is necessary for *every* project you want to
install there, then the system setup is somehow broken
I think if there is something broken with Cori, loads of other users would
run into the same problem -- that doesn't mean that everything's right
either, for example: one of the libraries used by deal.II might be broken.
If there is a way find out where deal.II's build system gets its link-time
flags (i.e. is there a verbose mode? can be get more information about how
cmake detects its environment?)
> so I suspect that there is a reason why the compiler requires linking
with this project, but I don't know why
This is the first build where we needed to add this library explicitly. And
looking at past tickets, I can only find a hand full of occurrences of this
error.
The ATP module is loaded by default (and the cray compiler wrappers link to
it automatically), so I am also confused why this step is necessary. The
only things that I can think of are listed above. I agree with them that it
makes sense to try and debug why this and find out why their build needs
something special. I was hoping that you (i.e. the deal.II developers)
would know that this is an issue with Cray systems already. Alas, it seems
that this is a new problem for you also.
But I am available to work with you directly -- however I cannot debug this
on my own (as the cmake setup is pretty huge!).
Cheers,
Johannes
On Monday, August 24, 2020 at 4:15:50 PM UTC-7 Wolfgang Bangerth wrote:
> On 8/24/20 3:40 PM, Aaditya Lakshmanan wrote:
> >
> > I am not sure what the above means. I contacted support at NERSC for
> help and
> > he responded as follows :
> >
> -
> > The problem is that somewhere in the cmake files it's missing:
> > ```
> > find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)
> > ```
> > and then you need to add
> > ```
> > target_link_libraries( ${ATP_SIGHANDLER_LIBRARY})
> > ```
> > to the file that specifies the link step for `libdeal_II.g.so`
> >
> > I had a look at the cmake files, but it's a pretty complex setup. I
> think it
> > might be best to reach out to the developers again, and get them to
> > incorporate those changes for cray systems.
> >
> -
> >
>
> Aaditya -- that would help, but the question is why that is necessary.
> What
> does this library do, and why do we need to link with it? If this kind of
> change is necessary for *every* project you want to install there, then
> the
> system setup is somehow broken -- so I suspect that there is a reason why
> the
> compiler requires linking with this project, but I don't know why. Can you
> ask
> you system support why this is necessary and why the compiler doesn't link
> these libraries in itself?
>
> Best
> W.
>
> --
>
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>
--
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Re: [deal.II] deal.ii Installation : expand_instantiations Error
On 8/24/20 3:40 PM, Aaditya Lakshmanan wrote:
I am not sure what the above means. I contacted support at NERSC for help and
he responded as follows :
-
The problem is that somewhere in the cmake files it's missing:
```
find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)
```
and then you need to add
```
target_link_libraries( ${ATP_SIGHANDLER_LIBRARY})
```
to the file that specifies the link step for `libdeal_II.g.so`
I had a look at the cmake files, but it's a pretty complex setup. I think it
might be best to reach out to the developers again, and get them to
incorporate those changes for cray systems.
-
Aaditya -- that would help, but the question is why that is necessary. What
does this library do, and why do we need to link with it? If this kind of
change is necessary for *every* project you want to install there, then the
system setup is somehow broken -- so I suspect that there is a reason why the
compiler requires linking with this project, but I don't know why. Can you ask
you system support why this is necessary and why the compiler doesn't link
these libraries in itself?
Best
W.
--
Wolfgang Bangerth email: bange...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/
--
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Re: [deal.II] deal.ii Installation : expand_instantiations Error
Hi Matthias,
I followed the steps you suggested so that expand_instantiations gave
the output :
Usage:
expand_instantiations class_list_files < in_file > out_file
after which I changed to the regular build directory for building(all
performed on an interactive compute node ) as
cmake -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment -DCMAKE_C_COMPILER=cc
-DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn -DDEAL_II_WITH_MPI=ON
-DDEAL_II_WITH_PETSC=ON -DDEAL_II_WITH_P4EST=ON -DDEAL_II_WITH_LAPACK=ON
-DCMAKE_INSTALL_PREFIX=/global/project/projectdirs/m2360/packagesCPFE/dealii_trial
../dealii
which ran fine, after which the installation process
make -j 8 install
resulted in the following error :
[100%] Built target obj_fe_debug
[100%] Linking CXX shared library ../lib/libdeal_II.g.so
/usr/bin/ld: cannot find -lAtpSigHandler
/usr/bin/ld: cannot find -lAtpSigHCommData
make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1283:
lib/libdeal_II.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:2978: source/CMakeFiles/deal_II.dir/all]
Error 2
make[1]: *** Waiting for unfinished jobs
I am not sure what the above means. I contacted support at NERSC for help
and he responded as follows :
-
The problem is that somewhere in the cmake files it's missing:
```
find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)
```
and then you need to add
```
target_link_libraries( ${ATP_SIGHANDLER_LIBRARY})
```
to the file that specifies the link step for `libdeal_II.g.so`
I had a look at the cmake files, but it's a pretty complex setup. I think
it might be best to reach out to the developers again, and get them to
incorporate those changes for cray systems.
-
Thank you for your help.
Best,
Aaditya
On Sunday, August 23, 2020 at 3:06:31 PM UTC-4 Matthias Maier wrote:
> Hi,
>
> CMake's cross compilation features are unfortunately a bit limited. To
> work around this you have to create an executable
> "expand_instantiations" separately by doing for example the following in
> the source directory:
>
> $ mkdir build-executable
> $ cd build-executable
> $ cmake ..
> $ make expand_instantiations_exe
>
> After that export the executable to your path:
>
> $ export PATH="$PWD/bin:$PATH"
>
> when you now run "expand_instantiations" in your command prompt you
> should get a help message:
>
> $ expand_instantiations
> Usage:
> expand_instantiations class_list_files < in_file > out_file
>
> If all that works out switch to the actual build directory (in the same
> terminal) and compile.
>
> This should take care of the following error:
>
> > /bin/sh: expand_instantiations: command not found
> > make[2]: ***
>
> Best,
> Matthias
>
>
>
>
--
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[deal.II] Postdoc position at Kassel University
At the University of Kassel, Institute of Mathematics – Analysis and Applied Mathematics (Prof. Dr. Friedmann) the following position is to be filled on October 1st, 2020: *Research Assistant, EG 13 TV-H, *a part-time position ( 75% of a full-time employee). The task will be to work on the development and implementation of advanced numerical methods for convection diffusion systems for pharmacological applications in ophthalmology. Our group is working with finite elements in deal.ii on the realization of (patho)physiological processes in the eye. The developed techniques are part of an interdisciplinary research project together with the Heidelberg University Eye Clinic and the David J. Apple International Laboratory for Ocular Pathology. Knowledge of finite element methods and prior software experience in deal.ii, C++ and parallel code development is required. Applicants must have a Doctorate in Mathematics, Computational Sciences or related fields. For more information about the project and team visit https://ganymed.math.uni-heidelberg.de/~elfi/. To apply, please visit https://stellen.uni-kassel.de/jobposting/f4a18a3b28c55b2f40b160ef1b15218af62084570 Best wishes, Elfi -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/23a2523e-e7a9-4b75-90b5-6276d615b0ddn%40googlegroups.com.
[deal.II] deal.II Newsletter #131
Hello everyone! This is deal.II newsletter #131. It automatically reports recently merged features and discussions about the deal.II finite element library. ## Below you find a list of recently proposed or merged features: #10840: Use DiscreteTime in step-52 (proposed by rezarastak) https://github.com/dealii/dealii/pull/10840 #10839: Move line (proposed by peterrum; merged) https://github.com/dealii/dealii/pull/10839 #10838: Destroy tmp matrix in mmult. (proposed by richardschu) https://github.com/dealii/dealii/pull/10838 #10837: Ignore differences in line endings on Windows and Linux. (proposed by bangerth; merged) https://github.com/dealii/dealii/pull/10837 #10836: DataOut::write_vtu_with_pvtu_record(): prints the path name if file cannot be opened (proposed by peterrum; merged) https://github.com/dealii/dealii/pull/10836 #10835: Optional argument for DEAL_II_PICKUP_TESTS (proposed by peterrum) https://github.com/dealii/dealii/pull/10835 #10834: Run test suite also for json files (proposed by peterrum) https://github.com/dealii/dealii/pull/10834 #10781: Simplify some code. (proposed by bangerth; merged) https://github.com/dealii/dealii/pull/10781 #10750: CMake: Fix static executable build for cmake 3.9 and newer (proposed by tamiko; merged) https://github.com/dealii/dealii/pull/10750 ## And this is a list of recently opened or closed discussions: #10832: build issue (closed) https://github.com/dealii/dealii/issues/10832 #9184: Build of static library possibly broken (closed) https://github.com/dealii/dealii/issues/9184 A list of all major changes since the last release can be found at https://www.dealii.org/developer/doxygen/deal.II/recent_changes.html. Thanks for being part of the community! Let us know about questions, problems, bugs or just share your experience by writing to dealii@googlegroups.com, or by opening issues or pull requests at https://www.github.com/dealii/dealii. Additional information can be found at https://www.dealii.org/. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/5f43e412.1c69fb81.fcf1e.b544SMTPIN_ADDED_MISSING%40gmr-mx.google.com.
