Deal ii installation via candi

[Narasimhan Swaminathan IITM]

I am truing to install dealII(9.5.1) via candi.sh. I am able to install it without Trilinos. When I uncomment Trilinos and try to install, I get the following error (pasted below). The OS is 24.04 ubuntu. Could I please get some help? If there is anything else I need to check, please let me know.

Thank you for your help.

[ 28%] Linking C shared library libzoltan.so
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_sset_var.c.o
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_side_set.c.o
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_side_set_dist_fact.c.o
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_sset_var_tab.c.o
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_tab.c.o
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_names.c.o
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_param.c.o
[ 28%] Building C object packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_name.c.o
[ 28%] Linking C shared library libexodus.so
[ 28%] Built target zoltan
[ 28%] Built target exodus
make: *** [Makefile:166: all] Error 2
Failure with exit status: 2
Exit message: There was a problem building trilinos 13-2-0.

[Wolfgang Bangerth]

On 5/9/24 09:37, Narasimhan Swaminathan IITM wrote:
>
>
> [ 28%] Linking C shared library libzoltan.so
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_sset_var.c.o
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_side_set.c.o
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_side_set_dist_fact.c.o
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_sset_var_tab.c.o
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_tab.c.o
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_names.c.o
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_param.c.o
> [ 28%] Building C object
> packages/seacas/libraries/exodus/CMakeFiles/exodus.dir/src/deprecated/ex_put_var_name.c.o
> [ 28%] Linking C shared library libexodus.so
> [ 28%] Built target zoltan
> [ 28%] Built target exodus
> make: *** [Makefile:166: all] Error 2
> Failure with exit status: 2

The error is likely higher up, and is most probably that you are compiling in
parallel (candi -j 8, for example) but running out of memory. Try reducing the
degree of parallelism and just run candi again.

Best
W.

--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[Narasimhan Swaminathan IITM]

Thank you. 

I initially tried ./candi.sh - j 8, then I have tried -j 4, -j 3 and -j 1. All of them quit at various times (% completion) and with slightly different errors. In all cases, it did say 

"Finished configuring Trilinos!

-- Configuring done (14.7s)
-- Generating done (1.2s)
"

The errors with various levels of parallelization were:

-j 1 

----------------------------------------------------------------------------------

"make[2]: *** [packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/build.make:188: packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_MemoryPool.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:5507: packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/all] Error 2

make: *** [Makefile:166: all] Error 2
"

------------------------------------------

-j 3

"[  6%] Building C object packages/zoltan/src/CMakeFiles/zoltan.dir/zz/zz_back_trace.c.o
[  6%] Building C object packages/zoltan/src/CMakeFiles/zoltan.dir/zz/zz_util.c.o
[  6%] Linking C shared library libzoltan.so
[  6%] Built target zoltan

make: *** [Makefile:166: all] Error 2
"

-j 4

"[ 10%] Building C object packages/zoltan/src/CMakeFiles/zoltan.dir/zz/zz_back_trace.c.o
[ 10%] Building C object packages/zoltan/src/CMakeFiles/zoltan.dir/zz/zz_util.c.o
[ 10%] Linking C shared library libzoltan.so
[ 10%] Built target zoltan

make: *** [Makefile:166: all] Error 2
Failure with exit status: 2

"

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[Wolfgang Bangerth]

On 5/9/24 11:29, Narasimhan Swaminathan IITM wrote:
>
> The errors with various levels of parallelization were:
>
> -j 1
> ----------------------------------------------------------------------------------
> "make[2]: ***
> [packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/build.make:188:
> packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/impl/Kokkos_MemoryPool.cpp.o] Error 1
> make[1]: *** [CMakeFiles/Makefile2:5507:
> packages/kokkos/core/src/CMakeFiles/kokkoscore.dir/all] Error 2
> make: *** [Makefile:166: all] Error 2

Kokkos is such a memory hog to compile :-( How much memory do you have on your
system?

[Narasimhan Swaminathan IITM]

The system has 64GB RAM

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[Wolfgang Bangerth]

On 5/9/24 11:35, Narasimhan Swaminathan IITM wrote:
> The system has 64GB RAM

That should be plenty. Do you have a ULIMIT set?

In the error messages, all you show is the output from 'make', which simply
reports "a compile job failed". Can you show what the compiler actually said,
somewhere higher up in the output?

[Narasimhan Swaminathan IITM]

OK. I am attaching the output of  ./candi.sh -j 1 as an output.txt file. I hope that is ok. I was not sure what I should look for higher up in the output.

Thank you

SN

[Wolfgang Bangerth]

On 5/9/24 12:10, Narasimhan Swaminathan IITM wrote:
> OK. I am attaching the output of  ./candi.sh -j 1 as an output.txt file. I
> hope that is ok. I was not sure what I should look for higher up in the output.

Oh, I see, it's not running out of memory after all. I just can't compile
Trilinos:

/home/narasimhan-swaminathan/Documents/Research/Software/Deal_II/candi/install/tmp/unpack/Trilinos-trilinos-release-13-2-0/packages/kokkos/core/src/impl/Kokkos_MemoryPool.cpp:112:48:
error: ‘uint32_t’ has not been declared
112 | void _print_memory_pool_state(std::ostream& s, uint32_t const*
sb_state_ptr,
| ^~~~~~~~

and later

src/impl/Kokkos_MemoryPool.cpp:49:1: note: ‘uint32_t’ is defined in header
‘<cstdint>’; did you forget to ‘#include <cstdint>’?
48 | #include <sstream>
+++ |+#include <cstdint>
49 |

So the Trilinos folks forgot to #include a necessary file; this may have
worked with some compilers in the past but apparently it does not work with
your compiler. I *suspect* that that is fixed in newer Trilinos versions, but
you can also head the suggestion of adding <cstdint> to the mentioned file by
hand and fix the problem yourself. The file to fix is
/home/narasimhan-swaminathan/Documents/Research/Software/Deal_II/candi/install/tmp/unpack/Trilinos-trilinos-release-13-2-0/packages/kokkos/core/src/impl/Kokkos_MemoryPool.cpp

[Narasimhan Swaminathan IITM]

I added the header in the upack directory, but I think the issue is, everytime ./candi.sh is run, it unpacks (unzips) it from a tar.gz file into the unpack folder and then uses that. So even if I change it in the unpack folder, it uncompresses the file from a tar.gz file and uses that.

So I tried to change the file (add the #include <cstdint>) and then tar.gzed the folder and then put it back in the folder which had the tar.gz with the same name and tried to run. It did this "903b797cddfdd82b0516d4659e90f738 does not match given checksum 099680cd3660dba5ec447ddc50a8406c" and then redownloaded a new version and tried to installed it (which was unsuccessful for the same reason). 

Is there a way to make candi.sh to install from the unpack folder (where the file was changed), without again unpacking it from the tar.gzed version?

Thank you

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[Wolfgang Bangerth]

On 5/9/24 13:10, Narasimhan Swaminathan IITM wrote:
>
> Is there a way to make candi.sh to install from the unpack folder (where the
> file was changed), without again unpacking it from the tar.gzed version?

I must admit that I don't know candi well enough. But you can select which
Trilinos version to use in candi.cfg; perhaps try selecting a different version?

[Narasimhan Swaminathan IITM]

Sure. I will try that. Thank you.

SN

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[Narasimhan Swaminathan IITM]

I tried using Trilinos versions 12, and also 14. Both did not compile. 

14 did have that #include <cstdint> in the Trilinos_MemoryPool.cpp file, but it still did not compile. I then simply installed sudo apt-get install libdeal.ii-dev. This installed 9.5.1. Except I think, Symengine ( I could not run Step-71). Step-72 runs properly. 

I think I'll use this for now.

Thank you

SN

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[Wolfgang Bangerth]

On 5/10/24 10:10, Narasimhan Swaminathan IITM wrote:
> **

>
> I tried using Trilinos versions 12, and also 14. Both did not compile.
> 14 did have that #include <cstdint> in the Trilinos_MemoryPool.cpp file, but
> it still did not compile. I then simply installed sudo apt-get install
> libdeal.ii-dev. This installed 9.5.1. Except I think, Symengine ( I could not
> run Step-71). Step-72 runs properly.
> I think I'll use this for now.

Ah yes, that's definitely the easiest of all options :-)

[Gerald Marewo]

Dear SN,

How about compiling from source as usual. Either ./configure, make, make install or cmake ., make install?

Regards,

Gerald.