Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-29 Thread Johannes Blaschke
Hi y'all,

I just wanted to update y'all on what we've learned so far:

1) message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}") 

Shows `/opt/cray/pe/atp/2.1.3/libApp` as one of the entries -- this is the 
home of AtpSigHandler.so, so (in theory) cmake should find it.

2) Including `find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)` 
gives the following error:

CMake Error: The following variables are used in this project, but they are 
set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake 
files:
ATP_SIGHANDLER_LIBRARY
linked by target "deal_II.g" in directory 
/global/project/projectdirs/m2360/packagesCPFE/dealii/source
linked by target "deal_II" in directory 
/global/project/projectdirs/m2360/packagesCPFE/dealii/source

-- Configuring incomplete, errors occurred

When adding `ATP_SIGHANDLER_LIBRARY` to target_link_library in 
source/CMakeLists.txt

My theory is that find_library is not detecting libAtpSigHandler.so -- but 
why?

Cheers,
Johannes

On Thursday, August 27, 2020 at 3:06:12 PM UTC-7 aadit...@gmail.com wrote:

> Hi Matthias,
>I tried the cmake and make on the login and interactive compute nodes 
> with other versions of zlib modules. In all cases I obtain the same error 
> as I did earlier :
>
> [100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
> [100%] Linking CXX shared library ../lib/libdeal_II.so
> /usr/bin/ld: cannot find -lAtpSigHandler
> /usr/bin/ld: cannot find -lAtpSigHCommData
> make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1274: 
> lib/libdeal_II.so] Error 1
> make[1]: *** [CMakeFiles/Makefile2:2879: 
> source/CMakeFiles/deal_II.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
>
>
> For all the versions of zlib modules loaded, in the 'detailed.log' file 
> the lines involving zlib dependencies are as follows :
>
> # DEAL_II_WITH_ZLIB set up with external dependencies
> # ZLIB_VERSION = 1.2.11
> # ZLIB_INCLUDE_DIRS = /usr/include
> # ZLIB_LIBRARIES = /usr/lib64/libz.so 
>
> I performed a make clean and deleted the files in the build directory 
> before running cmake with a different zlib module.
>
> Based on one of your earlier suggestions I included the following 
> lines(with help from Johannes) in 'CMakeLists.txt' :
>
>
> ---
> ENABLE_LANGUAGE_OPTIONAL(Fortran)
>
> # Modification start - Lines included based on Matthias suggestion
>
> message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}")
> message("Link libraries: ${CMAKE_CXX_IMPLICIT_LINK_LIBRARIES}")
> message(FATAL_ERROR "exit")
> # Modification end
>
>
> #---
>
>
> VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_deal_ii.cmake)
>
>
> ---
>  
>
> and then executing cmake from the main build directory resulted in the 
> following output just before exiting :
>
> Link directories: /opt/cray/pe/hdf5/
> 1.10.2.0/intel/16.0/lib;/opt/cray/dmapp/default/lib64;/opt/cray/pe/mpt/7.7.14/gni/mpich-intel/16.0/lib;/global/common/sw/cray/sles15/x86_64/zlib/1.2.11/gcc/8.2.0/pep2pal/lib;/opt/cray/pe/atp/2.1.3/libApp;/global/common/sw/cray/cnl7/haswell/petsc/3.11.2/intel/19.0.3.199/hocbntp/lib;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/2jbygqt/lib;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/vnkv5xn/lib;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/lib;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/j73evxt/lib;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/4m7cu62/lib;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/dkb63mv/lib;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin;/usr/lib64/gcc/x86_64-suse-linux/7;/usr/lib64;/lib64;/usr/x86_64-suse-linux/lib;/lib;/usr/lib
> Link libraries: 
> hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5_hl_cpp;hdf5_cpp;mpich_intel;mpichcxx_intel;stdc++;imf;m;ifcoremt;ifport;pthread;imf;svml;irng;stdc++;m;ipgo;decimal;cilkrts;stdc++;gcc;gcc_s;irc;svml;c;gcc;gcc_s;irc_s;dl;c
> CMake Error at CMakeLists.txt:102 (message):
>   exit
>
> -- Configuring incomplete, errors occurred!
>  
> From the Link libraries output it looks like AtpSigHandler and 
> AtpSigHCommData are picked up. Is there anything else I can try? Thank you.
>
> Best,
> Aaditya
>  
> On Wednesday, August 26, 2020 at 5:31:53 PM UTC-4 Aaditya Lakshmanan wrote:
>
>> Hi,
>>   Compiling deal.ii with DEAL_II_WITH_ZLIB=OFF and subsequently make -j 
>> 32 install gives the same error as earlier :
>>
>> [100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
>> [100%] Linking CXX shared 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-27 Thread Aaditya Lakshmanan
Hi Matthias,
   I tried the cmake and make on the login and interactive compute nodes 
with other versions of zlib modules. In all cases I obtain the same error 
as I did earlier :

[100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
[100%] Linking CXX shared library ../lib/libdeal_II.so
/usr/bin/ld: cannot find -lAtpSigHandler
/usr/bin/ld: cannot find -lAtpSigHCommData
make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1274: 
lib/libdeal_II.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:2879: source/CMakeFiles/deal_II.dir/all] 
Error 2
make[1]: *** Waiting for unfinished jobs


For all the versions of zlib modules loaded, in the 'detailed.log' file the 
lines involving zlib dependencies are as follows :

# DEAL_II_WITH_ZLIB set up with external dependencies
# ZLIB_VERSION = 1.2.11
# ZLIB_INCLUDE_DIRS = /usr/include
# ZLIB_LIBRARIES = /usr/lib64/libz.so 

I performed a make clean and deleted the files in the build directory 
before running cmake with a different zlib module.

Based on one of your earlier suggestions I included the following 
lines(with help from Johannes) in 'CMakeLists.txt' :

---
ENABLE_LANGUAGE_OPTIONAL(Fortran)

# Modification start - Lines included based on Matthias suggestion

message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}")
message("Link libraries: ${CMAKE_CXX_IMPLICIT_LINK_LIBRARIES}")
message(FATAL_ERROR "exit")
# Modification end


#---


VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_deal_ii.cmake)

---
 

and then executing cmake from the main build directory resulted in the 
following output just before exiting :

Link directories: 
/opt/cray/pe/hdf5/1.10.2.0/intel/16.0/lib;/opt/cray/dmapp/default/lib64;/opt/cray/pe/mpt/7.7.14/gni/mpich-intel/16.0/lib;/global/common/sw/cray/sles15/x86_64/zlib/1.2.11/gcc/8.2.0/pep2pal/lib;/opt/cray/pe/atp/2.1.3/libApp;/global/common/sw/cray/cnl7/haswell/petsc/3.11.2/intel/19.0.3.199/hocbntp/lib;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/2jbygqt/lib;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/vnkv5xn/lib;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/lib;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/j73evxt/lib;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/4m7cu62/lib;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/dkb63mv/lib;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin;/usr/lib64/gcc/x86_64-suse-linux/7;/usr/lib64;/lib64;/usr/x86_64-suse-linux/lib;/lib;/usr/lib
Link libraries: 
hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5_hl_cpp;hdf5_cpp;mpich_intel;mpichcxx_intel;stdc++;imf;m;ifcoremt;ifport;pthread;imf;svml;irng;stdc++;m;ipgo;decimal;cilkrts;stdc++;gcc;gcc_s;irc;svml;c;gcc;gcc_s;irc_s;dl;c
CMake Error at CMakeLists.txt:102 (message):
  exit

-- Configuring incomplete, errors occurred!
 
>From the Link libraries output it looks like AtpSigHandler and 
AtpSigHCommData are picked up. Is there anything else I can try? Thank you.

Best,
Aaditya
 
On Wednesday, August 26, 2020 at 5:31:53 PM UTC-4 Aaditya Lakshmanan wrote:

> Hi,
>   Compiling deal.ii with DEAL_II_WITH_ZLIB=OFF and subsequently make -j 32 
> install gives the same error as earlier :
>
> [100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
> [100%] Linking CXX shared library ../lib/libdeal_II.so
> /usr/bin/ld: cannot find -lAtpSigHandler
> /usr/bin/ld: cannot find -lAtpSigHCommData
> make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1274: 
> lib/libdeal_II.so] Error 1
> make[1]: *** [CMakeFiles/Makefile2:2879: 
> source/CMakeFiles/deal_II.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
>
> So I will try with another zlib module than the one originally used. I 
> have attached the 'detalied.log' file for my most recent attempt.
>
> Best,
> Aaditya
>
> On Wednesday, August 26, 2020 at 3:07:24 PM UTC-4 Matthias Maier wrote:
>
>>
>> On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke  
>> wrote: 
>>
>> > HI Matthias, 
>> > 
>> > thanks for your input -- you might be onto something RE ld 
>> > 
>> > We use a wrapper script for ld: 
>> > ``` 
>> > blaschke@cori06:~> which ld 
>> > /global/common/cori/software/altd/2.0/bin/ld 
>> > ``` 
>> > which is managed by the ALTD module (Automatic Library Tracking 
>> Database). 
>> > Using the system linker (which is what cmake is picking up) isn't 
>> usually a 
>> > problem, but in this case it might be. I checked Aaditya's loaded 
>> modules 
>> > and ALTD is in there, so CMake should be picking it up. How does 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Aaditya Lakshmanan
Hi,
  Compiling deal.ii with DEAL_II_WITH_ZLIB=OFF and subsequently make -j 32 
install gives the same error as earlier :

[100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
[100%] Linking CXX shared library ../lib/libdeal_II.so
/usr/bin/ld: cannot find -lAtpSigHandler
/usr/bin/ld: cannot find -lAtpSigHCommData
make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1274: 
lib/libdeal_II.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:2879: source/CMakeFiles/deal_II.dir/all] 
Error 2
make[1]: *** Waiting for unfinished jobs

So I will try with another zlib module than the one originally used. I have 
attached the 'detalied.log' file for my most recent attempt.

Best,
Aaditya

On Wednesday, August 26, 2020 at 3:07:24 PM UTC-4 Matthias Maier wrote:

>
> On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke  
> wrote:
>
> > HI Matthias,
> >
> > thanks for your input -- you might be onto something RE ld
> >
> > We use a wrapper script for ld:
> > ```
> > blaschke@cori06:~> which ld
> > /global/common/cori/software/altd/2.0/bin/ld
> > ```
> > which is managed by the ALTD module (Automatic Library Tracking 
> Database). 
> > Using the system linker (which is what cmake is picking up) isn't 
> usually a 
> > problem, but in this case it might be. I checked Aaditya's loaded 
> modules 
> > and ALTD is in there, so CMake should be picking it up. How does CMake 
> > detect the linker? Is it just a question of adding 
> `-DCMAKE_LINKER=$(which 
> > ld)`?
>
> Yes, setting CMAKE_LINKER would be an option. But typically CMake just
> invokes the compiler wrapper which should do the right thing...
>
> Best,
> Matthias
>

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   
/global/project/projectdirs/m2360/packagesCPFE/dealii_trial
#CMAKE_SOURCE_DIR:   
/global/project/projectdirs/m2360/packagesCPFE/dealii
#(version 9.1.1, shortrev 777cf92a41)
#CMAKE_BINARY_DIR:   
/global/project/projectdirs/m2360/packagesCPFE/build
#CMAKE_CXX_COMPILER: Intel 19.0.0.20190206 on platform 
CrayLinuxEnvironment x86_64
#/opt/cray/pe/craype/2.6.2/bin/CC
#CMAKE_C_COMPILER:   /opt/cray/pe/craype/2.6.2/bin/cc
#CMAKE_Fortran_COMPILER: /opt/cray/pe/craype/2.6.2/bin/ftn
#CMAKE_GENERATOR:Unix Makefiles
#
#CROSSCOMPILING!
#
#  Base configuration (prior to feature configuration):
#DEAL_II_CXX_FLAGS:-fpic -ansi -w2 -diag-disable=remark 
-wd21 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 
-wd1418 -wd1478 -wd1572 -wd2259 -wd2536 -wd2651 -wd3415 -wd15531 -wd111 -wd128 
-wd185 -wd186 -wd280 -std=c++17
#DEAL_II_CXX_FLAGS_RELEASE:-O2 -no-ansi-alias -ip -funroll-loops
#DEAL_II_CXX_FLAGS_DEBUG:  -O0 -g -gdwarf-2 -grecord-gcc-switches
#DEAL_II_LINKER_FLAGS: -Wl,--as-needed -shared-intel -rdynamic
#DEAL_II_LINKER_FLAGS_RELEASE:
#DEAL_II_LINKER_FLAGS_DEBUG:
#DEAL_II_DEFINITIONS:
#DEAL_II_DEFINITIONS_RELEASE:
#DEAL_II_DEFINITIONS_DEBUG:DEBUG
#DEAL_II_USER_DEFINITIONS:
#DEAL_II_USER_DEFINITIONS_REL:
#DEAL_II_USER_DEFINITIONS_DEB: DEBUG
#DEAL_II_INCLUDE_DIRS
#DEAL_II_USER_INCLUDE_DIRS:
#DEAL_II_BUNDLED_INCLUDE_DIRS:
#DEAL_II_LIBRARIES:
#DEAL_II_LIBRARIES_RELEASE:
#DEAL_II_LIBRARIES_DEBUG:
#DEAL_II_COMPILER_VECTORIZATION_LEVEL: 0
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#  ( DEAL_II_WITH_ARPACK = OFF )
#  ( DEAL_II_WITH_ASSIMP = OFF )
#DEAL_II_WITH_BOOST set up with bundled packages
#BOOST_BUNDLED_INCLUDE_DIRS = 
/global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/boost-1.62.0/include
#BOOST_LIBRARIES = rt
#DEAL_II_WITH_COMPLEX_VALUES = ON
#  ( DEAL_II_WITH_CUDA = OFF )
#DEAL_II_WITH_CXX14 = ON
#DEAL_II_WITH_CXX17 = ON
#  ( DEAL_II_WITH_GINKGO = OFF )
#  ( DEAL_II_WITH_GMSH = OFF )
#  ( DEAL_II_WITH_GSL = OFF )
#  ( DEAL_II_WITH_HDF5 = OFF )
#DEAL_II_WITH_LAPACK set up with external dependencies
#LAPACK_WITH_64BIT_BLAS_INDICES = OFF
#LAPACK_LINKER_FLAGS 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Matthias Maier


On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke  
wrote:

> HI Matthias,
>
> thanks for your input -- you might be onto something RE ld
>
> We use a wrapper script for ld:
> ```
> blaschke@cori06:~> which ld
> /global/common/cori/software/altd/2.0/bin/ld
> ```
> which is managed by the ALTD module (Automatic Library Tracking Database). 
> Using the system linker (which is what cmake is picking up) isn't usually a 
> problem, but in this case it might be. I checked Aaditya's loaded modules 
> and ALTD is in there, so CMake should be picking it up. How does CMake 
> detect the linker? Is it just a question of adding `-DCMAKE_LINKER=$(which 
> ld)`?

Yes, setting CMAKE_LINKER would be an option. But typically CMake just
invokes the compiler wrapper which should do the right thing...

Best,
Matthias

-- 
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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Matthias Maier


On Wed, Aug 26, 2020, at 13:01 CDT, Aaditya Lakshmanan  
wrote:

> Hi, 
>   zlib(version 1.2.11) was already loaded as a module in all my previous 
> compilation attempts. I will try it by setting DEAL_II_WITH_ZLIB=OFF but I 
> am not sure why the path to zlib libraries is picked up from /usr . Thanks 
> for the suggestion.

This is probably simply a faulty zlib module shipped with zlib. In order
to force cmake to pick up the correct library it might be easiest to use
"CMAKE_PREFIX_PATH" like so:

  -DCMAKE_PREFIX_PATH=/path/to/the/zlib/module/

If that doesn't help then you can specify zlib by hand:

  -DDEAL_II_WITH_ZLIB=ON -DZLIB_INCLUDE_DIRS=/[...]/include 
-DZLIB_LIBRARIES=/[...]/libz.so

Best,
Matthias

-- 
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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Aaditya Lakshmanan
Hi, 
  zlib(version 1.2.11) was already loaded as a module in all my previous 
compilation attempts. I will try it by setting DEAL_II_WITH_ZLIB=OFF but I 
am not sure why the path to zlib libraries is picked up from /usr . Thanks 
for the suggestion.

Best,
Aaditya

On Wednesday, August 26, 2020 at 1:46:10 PM UTC-4 jpbla...@lbl.gov wrote:

> HI Matthias,
>
> thanks for your input -- you might be onto something RE ld
>
> We use a wrapper script for ld:
> ```
> blaschke@cori06:~> which ld
> /global/common/cori/software/altd/2.0/bin/ld
> ```
> which is managed by the ALTD module (Automatic Library Tracking Database). 
> Using the system linker (which is what cmake is picking up) isn't usually a 
> problem, but in this case it might be. I checked Aaditya's loaded modules 
> and ALTD is in there, so CMake should be picking it up. How does CMake 
> detect the linker? Is it just a question of adding `-DCMAKE_LINKER=$(which 
> ld)`?
>
> RE zlib: we have a zlib module. So maybe it's just a question of loading 
> that. Does CMake just detect zlib in the PATH? If so, doing a `module load 
> zlib` should be enough. Otherwise, is there a way to point CMake to the 
> zlib module directory?
>
> Cheers,
> Johannes
>
>
> On Wednesday, August 26, 2020 at 8:43:42 AM UTC-7 Matthias Maier wrote:
>
>> Thanks. 
>>
>> This looks mostly good. 
>>
>> In particular, the Lapack CMake module seems to pick up "AtpSigHandler" 
>> and "AtpSigHCommData": 
>>
>> 55 # DEAL_II_WITH_LAPACK set up with external dependencies 
>> 56 # LAPACK_WITH_64BIT_BLAS_INDICES = OFF 
>> 57 # LAPACK_LINKER_FLAGS = 
>> 58 # LAPACK_INCLUDE_DIRS = 
>> 59 # LAPACK_USER_INCLUDE_DIRS = 
>> 60 # LAPACK_LIBRARIES = 
>> /opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel6
>>  
>> 4/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiom
>>  
>> p5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl
>>  
>> ;c 
>>
>> One thing is peculiar: 
>>
>> 108 # DEAL_II_WITH_ZLIB set up with external dependencies 
>> 109 # ZLIB_VERSION = 1.2.11 
>> 110 # ZLIB_INCLUDE_DIRS = /usr/include 
>> 111 # ZLIB_LIBRARIES = /usr/lib64/libz.so 
>>
>> This library does not reside under /global and I doubt it has the right 
>> architecture. Would you mind disabling zlib support for the time being 
>> (-DDEAL_II_WITH_ZLIB=OFF)? Or reconfigure such that the correct zlib 
>> library is picked up? 
>>
>> Maybe this explains why the system linker /usr/bin/ld is used instead of 
>> one from the toolchain under /opt/cray/pe/craype/2.6.2/bin ... 
>>
>> Best, 
>> Matthias 
>>
>

-- 
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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Johannes Blaschke
HI Matthias,

thanks for your input -- you might be onto something RE ld

We use a wrapper script for ld:
```
blaschke@cori06:~> which ld
/global/common/cori/software/altd/2.0/bin/ld
```
which is managed by the ALTD module (Automatic Library Tracking Database). 
Using the system linker (which is what cmake is picking up) isn't usually a 
problem, but in this case it might be. I checked Aaditya's loaded modules 
and ALTD is in there, so CMake should be picking it up. How does CMake 
detect the linker? Is it just a question of adding `-DCMAKE_LINKER=$(which 
ld)`?

RE zlib: we have a zlib module. So maybe it's just a question of loading 
that. Does CMake just detect zlib in the PATH? If so, doing a `module load 
zlib` should be enough. Otherwise, is there a way to point CMake to the 
zlib module directory?

Cheers,
Johannes


On Wednesday, August 26, 2020 at 8:43:42 AM UTC-7 Matthias Maier wrote:

> Thanks.
>
> This looks mostly good.
>
> In particular, the Lapack CMake module seems to pick up "AtpSigHandler"
> and "AtpSigHCommData":
>
> 55 # DEAL_II_WITH_LAPACK set up with external dependencies 
> 56 # LAPACK_WITH_64BIT_BLAS_INDICES = OFF 
> 57 # LAPACK_LINKER_FLAGS = 
> 58 # LAPACK_INCLUDE_DIRS = 
> 59 # LAPACK_USER_INCLUDE_DIRS = 
> 60 # LAPACK_LIBRARIES = 
> /opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel6
>  
> 4/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiom
>  
> p5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl
>  
> ;c
>
> One thing is peculiar: 
>
> 108 # DEAL_II_WITH_ZLIB set up with external dependencies 
> 109 # ZLIB_VERSION = 1.2.11 
> 110 # ZLIB_INCLUDE_DIRS = /usr/include 
> 111 # ZLIB_LIBRARIES = /usr/lib64/libz.so 
>
> This library does not reside under /global and I doubt it has the right
> architecture. Would you mind disabling zlib support for the time being
> (-DDEAL_II_WITH_ZLIB=OFF)? Or reconfigure such that the correct zlib
> library is picked up?
>
> Maybe this explains why the system linker /usr/bin/ld is used instead of
> one from the toolchain under /opt/cray/pe/craype/2.6.2/bin ...
>
> Best,
> Matthias
>

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-26 Thread Matthias Maier
Thanks.

This looks mostly good.

In particular, the Lapack CMake module seems to pick up "AtpSigHandler"
and "AtpSigHCommData":

 55 #DEAL_II_WITH_LAPACK set up with external dependencies  
 
 56 #LAPACK_WITH_64BIT_BLAS_INDICES = OFF   
 
 57 #LAPACK_LINKER_FLAGS =  
 
 58 #LAPACK_INCLUDE_DIRS =  
 
 59 #LAPACK_USER_INCLUDE_DIRS = 
 
 60 #LAPACK_LIBRARIES = 
/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel6

4/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiom

p5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl
;c

One thing is peculiar: 

108 #DEAL_II_WITH_ZLIB set up with external dependencies
 
109 #ZLIB_VERSION = 1.2.11  
 
110 #ZLIB_INCLUDE_DIRS = /usr/include   
 
111 #ZLIB_LIBRARIES = /usr/lib64/libz.so 

This library does not reside under /global and I doubt it has the right
architecture. Would you mind disabling zlib support for the time being
(-DDEAL_II_WITH_ZLIB=OFF)? Or reconfigure such that the correct zlib
library is picked up?

Maybe this explains why the system linker /usr/bin/ld is used instead of
one from the toolchain under /opt/cray/pe/craype/2.6.2/bin ...

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-25 Thread Aaditya Lakshmanan
Hi Matthias,
   I have attached the 'detailed.log' file here. I will attempt what you 
suggested. Thank you.

Best,
Aaditya

On Tuesday, August 25, 2020 at 5:10:30 PM UTC-4 Matthias Maier wrote:

>
> On Tue, Aug 25, 2020, at 00:07 CDT, Johannes Blaschke  
> wrote:
>
> > But I am available to work with you directly -- however I cannot debug 
> this 
> > on my own (as the cmake setup is pretty huge!).
>
> Please have a look at the file `detailed.log` found in the build
> directory. It spells out the compiler, all compile flags and the full
> configured link interface. Do you see anything odd there?
>
> Aaditya, Johannes: Another point to check quickly is whether CMake
> itself does the right thing. Would you mind adding the following three
> lines to the main CMakeLists.txt file and examining the output?
>
> diff --git a/CMakeLists.txt b/CMakeLists.txt
> index ab24b8f477..dce1dcac08 100644
> --- a/CMakeLists.txt
> +++ b/CMakeLists.txt
> @@ -95,6 +95,10 @@ 
> VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_cached_variables.cmake)
> PROJECT(deal.II CXX C)
> ENABLE_LANGUAGE_OPTIONAL(Fortran)
>
> +message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}")
> +message("Link libraries: ${CMAKE_CXX_IMPLICIT_LINK_LIBRARIES}")
> +message(FATAL_ERROR "exit")
> +
> VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_deal_ii.cmake)
>
> VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_compiler_flags.cmake)
>
>
> I expect that the AtpSigHandler library should be listed there.
>
> Best,
> Matthias
>

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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   
/global/project/projectdirs/m2360/packagesCPFE/dealii_trial
#CMAKE_SOURCE_DIR:   
/global/project/projectdirs/m2360/packagesCPFE/dealii
#(version 9.1.1, shortrev 777cf92a41)
#CMAKE_BINARY_DIR:   
/global/project/projectdirs/m2360/packagesCPFE/build
#CMAKE_CXX_COMPILER: Intel 19.0.0.20190206 on platform 
CrayLinuxEnvironment x86_64
#/opt/cray/pe/craype/2.6.2/bin/CC
#CMAKE_C_COMPILER:   /opt/cray/pe/craype/2.6.2/bin/cc
#CMAKE_Fortran_COMPILER: /opt/cray/pe/craype/2.6.2/bin/ftn
#CMAKE_GENERATOR:Unix Makefiles
#
#CROSSCOMPILING!
#
#  Base configuration (prior to feature configuration):
#DEAL_II_CXX_FLAGS:-fpic -ansi -w2 -diag-disable=remark 
-wd21 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 
-wd1418 -wd1478 -wd1572 -wd2259 -wd2536 -wd2651 -wd3415 -wd15531 -wd111 -wd128 
-wd185 -wd186 -wd280 -std=c++17
#DEAL_II_CXX_FLAGS_RELEASE:-O2 -no-ansi-alias -ip -funroll-loops
#DEAL_II_CXX_FLAGS_DEBUG:  -O0 -g -gdwarf-2 -grecord-gcc-switches
#DEAL_II_LINKER_FLAGS: -Wl,--as-needed -shared-intel -rdynamic
#DEAL_II_LINKER_FLAGS_RELEASE: 
#DEAL_II_LINKER_FLAGS_DEBUG:   
#DEAL_II_DEFINITIONS:  
#DEAL_II_DEFINITIONS_RELEASE:  
#DEAL_II_DEFINITIONS_DEBUG:DEBUG
#DEAL_II_USER_DEFINITIONS: 
#DEAL_II_USER_DEFINITIONS_REL: 
#DEAL_II_USER_DEFINITIONS_DEB: DEBUG
#DEAL_II_INCLUDE_DIRS  
#DEAL_II_USER_INCLUDE_DIRS:
#DEAL_II_BUNDLED_INCLUDE_DIRS: 
#DEAL_II_LIBRARIES:
#DEAL_II_LIBRARIES_RELEASE:
#DEAL_II_LIBRARIES_DEBUG:  
#DEAL_II_COMPILER_VECTORIZATION_LEVEL: 0
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#  ( DEAL_II_WITH_ARPACK = OFF )
#  ( DEAL_II_WITH_ASSIMP = OFF )
#DEAL_II_WITH_BOOST set up with bundled packages
#BOOST_BUNDLED_INCLUDE_DIRS = 
/global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/boost-1.62.0/include
#BOOST_LIBRARIES = rt
#DEAL_II_WITH_COMPLEX_VALUES = ON
#  ( DEAL_II_WITH_CUDA = OFF )
#DEAL_II_WITH_CXX14 = ON
#DEAL_II_WITH_CXX17 = ON
#  ( DEAL_II_WITH_GINKGO = OFF )
#  ( DEAL_II_WITH_GMSH = OFF )
#  ( DEAL_II_WITH_GSL = OFF )
#  ( DEAL_II_WITH_HDF5 = OFF )
#DEAL_II_WITH_LAPACK set up with external dependencies
#LAPACK_WITH_64BIT_BLAS_INDICES = OFF
#LAPACK_LINKER_FLAGS = 
#LAPACK_INCLUDE_DIRS = 
#LAPACK_USER_INCLUDE_DIRS = 
# 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-25 Thread Matthias Maier


On Tue, Aug 25, 2020, at 00:07 CDT, Johannes Blaschke  
wrote:

> But I am available to work with you directly -- however I cannot debug this 
> on my own (as the cmake setup is pretty huge!).

Please have a look at the file `detailed.log` found in the build
directory. It spells out the compiler, all compile flags and the full
configured link interface. Do you see anything odd there?

Aaditya, Johannes: Another point to check quickly is whether CMake
itself does the right thing. Would you mind adding the following three
lines to the main CMakeLists.txt file and examining the output?

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ab24b8f477..dce1dcac08 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -95,6 +95,10 @@ 
VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_cached_variables.cmake)
 PROJECT(deal.II CXX C)
 ENABLE_LANGUAGE_OPTIONAL(Fortran)
 
+message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}")
+message("Link libraries:   ${CMAKE_CXX_IMPLICIT_LINK_LIBRARIES}")
+message(FATAL_ERROR "exit")
+
 VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_deal_ii.cmake)
 
 VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_compiler_flags.cmake)


I expect that the AtpSigHandler library should be listed there.

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-25 Thread Matthias Maier
Would you mind quickly sending us the file `detailed.log` that you can
find in the build directory? This would help us a lot.

On Mon, Aug 24, 2020, at 16:40 CDT, Aaditya Lakshmanan  
wrote:

> [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

This implies that the linker (in this case "/usr/bin/ld" was invoked)
was not able to find the library "AtpSigHandler". So, your compiler
toolchain seems to do the right thing by adding

  -lAtpSigHandler -lAtpSigHCommData

to the link line but the linker does not know the correct library
location (which would typically be specified by -L<...>). This begs the
question whether "/usr/bin/ld" is actually the correct linker.


> The problem is that somewhere in the cmake files it's missing:
> ```
> find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)
> target_link_libraries( ${ATP_SIGHANDLER_LIBRARY})
> ```

It looks like that these two commands might work around the problem by
letting cmake add a "-L<...>" to the command line. You can give this a
shot with the following changes to source/CMakeLists.txt:


diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
index a6d85d8b68..86ca17d073 100644
--- a/source/CMakeLists.txt
+++ b/source/CMakeLists.txt
@@ -158,10 +158,12 @@ FOREACH(build ${DEAL_II_BUILD_TYPES})
   )
   ENDIF()
 
+  find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)
 
   TARGET_LINK_LIBRARIES(${DEAL_II_BASE_NAME}${DEAL_II_${build}_SUFFIX}
 ${DEAL_II_LIBRARIES_${build}}
 ${DEAL_II_LIBRARIES}
+${ATP_SIGHANDLER_LIBRARY}
 )
 
   FILE(MAKE_DIRECTORY



But I would rather prefer to figure out why our cmake configurations
(probably?) selects the wrong linker. In any case, please show us the
full contents of detailed.log

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-24 Thread Johannes Blaschke
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

2020-08-24 Thread Wolfgang Bangerth

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.

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-24 Thread Aaditya Lakshmanan
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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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-23 Thread Matthias Maier
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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Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-23 Thread Aaditya Lakshmanan
I tried compilation on the compute node with PrgEnv-intel loaded and 
including CMAKE_SYSTEM_NAME=CrayLinuxEnvironment in the cmake line. Upon 
make install it yielded the same error that I got earlier :

Scanning dependencies of target obj_numerics_inst
[ 41%] Generating data_out_dof_data.inst
/bin/sh: expand_instantiations: command not found
make[2]: *** 
[source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: 
source/numerics/data_out_dof_data.inst] Error 127
make[1]: *** [CMakeFiles/Makefile2:3074: 
source/numerics/CMakeFiles/obj_numerics_inst.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
[ 41%] Building CXX object 
bundled/muparser_v2_2_4/CMakeFiles/obj_muparser_release.dir/src/muParserInt.cpp.o
[ 41%] Building CXX object 
bundled/muparser_v2_2_4/CMakeFiles/obj_muparser_release.dir/src/muParserTest.cpp.o
[ 41%] Building CXX object 
bundled/muparser_v2_2_4/CMakeFiles/obj_muparser_release.dir/src/muParserTokenReader.cpp.o
[ 41%] Built target obj_muparser_debug
[ 41%] Built target obj_muparser_release
make: *** [Makefile:130: all] Error 2




On Sunday, August 23, 2020 at 11:52:15 AM UTC-4 Aaditya Lakshmanan wrote:

> Hi Timo,
> Thank you for sharing the link for cross-compilation of dealii. In the 
> same webpage there is a link 
>  to 
> information about cmake toolchain information and in that webpage I found 
> the following :
>
> Cross Compiling for the Cray Linux Environment 
>  
> 
>
> Cross compiling for compute nodes in the Cray Linux Environment can be 
> done without needing a separate toolchain file. 
> Specifying -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment on the CMake command 
> line will ensure that the appropriate build settings and search paths are 
> configured. The platform will pull its configuration from the current 
> environment variables and will configure a project to use the compiler 
> wrappers from the Cray Programming Environment’s PrgEnv-* modules if 
> present and loaded.
>
> The default configuration of the Cray Programming Environment is to only 
> support static libraries. This can be overridden and shared libraries 
> enabled by setting the CRAYPE_LINK_TYPE environment variable to dynamic.
>
> Running CMake without specifying CMAKE_SYSTEM_NAME 
> 
>  will 
> run the configure step in host mode assuming a standard Linux environment. 
> If not overridden, the PrgEnv-* compiler wrappers will end up getting used, 
> which if targeting the either the login node or compute node, is likely not 
> the desired behavior. The exception to this would be if you are building 
> directly on a NID instead of cross-compiling from a login node. If trying 
> to build software for a login node, you will need to either first unload 
> the currently loaded PrgEnv-* module or explicitly tell CMake to use the 
> system compilers in /usr/bin instead of the Cray wrappers. If instead 
> targeting a compute node is desired, just specify the CMAKE_SYSTEM_NAME 
> 
>  as 
> mentioned above.
>
>
> In my case I checked that PrgEnv-intel is one of the modules loaded by 
> default. I did specify CMAKE_SYSTEM_NAME earlier while running cmake, when 
> attempting the installation process on the login node and on the 
> interactive node. I will now try the following :
>
> 1) Compiling with PrgEnv-intel on the compute node with 
> CMAKE_SYSTEM_NAME=CrayLinuxEnvironment. 
>
> 2) Unloading PrgEnv-intel and compiling on the login node.
>
> Please let me know if you have any other suggestions. Thank you.
>
> Best,
>
> Aaditya
>
> On Saturday, August 22, 2020 at 3:23:49 PM UTC-4 Timo Heister wrote:
>
>> Hi Aaditya, 
>>
>> it looks like you are cross compiling due to the cray system you are 
>> on? I don't have first-hand experience, but I know some users have had 
>> success with it in the past. 
>>
>> The error message stems from the fact that we build a small tool 
>> "expand_instantiations" during the build process. If you are cross 
>> compiling, this executable obviously won't work, so the rest of the 
>> build fails. 
>>
>> Take a look at https://dealii.org/9.2.0/developers/porting.html 
>> (search for expand_instantiations) and let us know if that helps. 
>>
>> Best, 
>> Timo 
>>
>>
>> On Fri, Aug 21, 2020 at 2:52 PM Aaditya Lakshmanan 
>>  wrote: 
>> > 
>> > Hi Jean-Paul, 
>> > I cleaned the previous installation, deleted all the files generated in 
>> the build directory and attempted a fresh build process as follows : 
>> > 
>> > cmake -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment -DCMAKE_C_COMPILER=cc 
>> -DCMAKE_CXX_COMPILER=CC 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-23 Thread Aaditya Lakshmanan
Hi Timo,
Thank you for sharing the link for cross-compilation of dealii. In the 
same webpage there is a link 
 to 
information about cmake toolchain information and in that webpage I found 
the following :

Cross Compiling for the Cray Linux Environment 
 


Cross compiling for compute nodes in the Cray Linux Environment can be done 
without needing a separate toolchain file. 
Specifying -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment on the CMake command 
line will ensure that the appropriate build settings and search paths are 
configured. The platform will pull its configuration from the current 
environment variables and will configure a project to use the compiler 
wrappers from the Cray Programming Environment’s PrgEnv-* modules if 
present and loaded.

The default configuration of the Cray Programming Environment is to only 
support static libraries. This can be overridden and shared libraries 
enabled by setting the CRAYPE_LINK_TYPE environment variable to dynamic.

Running CMake without specifying CMAKE_SYSTEM_NAME 

 will 
run the configure step in host mode assuming a standard Linux environment. 
If not overridden, the PrgEnv-* compiler wrappers will end up getting used, 
which if targeting the either the login node or compute node, is likely not 
the desired behavior. The exception to this would be if you are building 
directly on a NID instead of cross-compiling from a login node. If trying 
to build software for a login node, you will need to either first unload 
the currently loaded PrgEnv-* module or explicitly tell CMake to use the 
system compilers in /usr/bin instead of the Cray wrappers. If instead 
targeting a compute node is desired, just specify the CMAKE_SYSTEM_NAME 

 as 
mentioned above.


In my case I checked that PrgEnv-intel is one of the modules loaded by 
default. I did specify CMAKE_SYSTEM_NAME earlier while running cmake, when 
attempting the installation process on the login node and on the 
interactive node. I will now try the following :

1) Compiling with PrgEnv-intel on the compute node with 
CMAKE_SYSTEM_NAME=CrayLinuxEnvironment. 

2) Unloading PrgEnv-intel and compiling on the login node.

Please let me know if you have any other suggestions. Thank you.

Best,

Aaditya

On Saturday, August 22, 2020 at 3:23:49 PM UTC-4 Timo Heister wrote:

> Hi Aaditya,
>
> it looks like you are cross compiling due to the cray system you are
> on? I don't have first-hand experience, but I know some users have had
> success with it in the past.
>
> The error message stems from the fact that we build a small tool
> "expand_instantiations" during the build process. If you are cross
> compiling, this executable obviously won't work, so the rest of the
> build fails.
>
> Take a look at https://dealii.org/9.2.0/developers/porting.html
> (search for expand_instantiations) and let us know if that helps.
>
> Best,
> Timo
>
>
> On Fri, Aug 21, 2020 at 2:52 PM Aaditya Lakshmanan
>  wrote:
> >
> > Hi Jean-Paul,
> > I cleaned the previous installation, deleted all the files generated in 
> the build directory and attempted a fresh build process as follows :
> >
> > 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 successfully after which I tried installing deal.ii via
> >
> > make -j 4 install
> >
> > which exited with the following error(just as before) :
> >
> > [ 40%] Building CXX object 
> bundled/muparser_v2_2_4/CMakeFiles/obj_muparser_release.dir/src/muParserTest.cpp.o
> > [ 40%] Generating data_out_dof_data.inst
> > /bin/sh: expand_instantiations: command not found
> > make[2]: *** 
> [source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: 
> source/numerics/data_out_dof_data.inst] Error 127
> > make[1]: *** [CMakeFiles/Makefile2:3074: 
> source/numerics/CMakeFiles/obj_numerics_inst.dir/all] Error 2
> > make[1]: *** Waiting for unfinished jobs
> > [ 41%] Built target obj_muparser_debug
> > [ 41%] Generating fe_abf.inst
> >
> > In the build/bin directory there is a file expand_instantiations of the 
> following type :
> >
> > expand_instantiations: ELF 64-bit LSB executable, x86-64, version 1 
> (SYSV), dynamically linked, interpreter /lib64/l, 
> BuildID[sha1]=3ee25c761ad827a88f618b972735b201bc6a2bbe, for GNU/Linux 
> 3.2.0, with debug_info, not 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-22 Thread Timo Heister
Hi Aaditya,

it looks like you are cross compiling due to the cray system you are
on? I don't have first-hand experience, but I know some users have had
success with it in the past.

The error message stems from the fact that we build a small tool
"expand_instantiations" during the build process. If you are cross
compiling, this executable obviously won't work, so the rest of the
build fails.

Take a look at https://dealii.org/9.2.0/developers/porting.html
(search for expand_instantiations) and let us know if that helps.

Best,
Timo


On Fri, Aug 21, 2020 at 2:52 PM Aaditya Lakshmanan
 wrote:
>
> Hi Jean-Paul,
>I cleaned the previous installation, deleted all the files generated in 
> the build directory and attempted a fresh build process as follows :
>
> 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 successfully after which I tried installing deal.ii via
>
> make -j 4 install
>
> which exited with the following error(just as before) :
>
> [ 40%] Building CXX object 
> bundled/muparser_v2_2_4/CMakeFiles/obj_muparser_release.dir/src/muParserTest.cpp.o
> [ 40%] Generating data_out_dof_data.inst
> /bin/sh: expand_instantiations: command not found
> make[2]: *** [source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: 
> source/numerics/data_out_dof_data.inst] Error 127
> make[1]: *** [CMakeFiles/Makefile2:3074: 
> source/numerics/CMakeFiles/obj_numerics_inst.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> [ 41%] Built target obj_muparser_debug
> [ 41%] Generating fe_abf.inst
>
> In the build/bin directory there is a file expand_instantiations of the 
> following type :
>
> expand_instantiations: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), 
> dynamically linked, interpreter /lib64/l, 
> BuildID[sha1]=3ee25c761ad827a88f618b972735b201bc6a2bbe, for GNU/Linux 3.2.0, 
> with debug_info, not stripped
>
> Is that the file you were referring to earlier? I have attached the 
> detailed.log file generated in the build directory. Let me know if you need 
> any more information from me. Thank you for your help.
>
> Best,
> Aaditya
>
> On Friday, August 21, 2020 at 2:03:59 PM UTC-4 Jean-Paul Pelteret wrote:
>>
>> Hi Aaditya,
>>
>> Great, let us know if that works for you. You should see the 
>> expand_instantiations binary appear in the “bin” sub-directory with your 
>> build folder. If it still doesn’t appear there, then perhaps you could 
>> create a new build directory and then post the configuration and full build 
>> logs that come from a fresh build. It could also be that this utility 
>> program is failing to build.
>>
>> Best,
>> Jean-Paul
>>
>> On 21 Aug 2020, at 19:37, Aaditya Lakshmanan  wrote:
>>
>> Hi Jean-Paul,
>>Thank you for your suggestion. I shall try the installation process with 
>> fewer processors(perhaps 4) and if even that doesn't work, then I will try 
>> it in serial.
>>
>> Best,
>> Aaditya
>>
>> On Friday, August 21, 2020 at 1:07:54 PM UTC-4 Jean-Paul Pelteret wrote:
>>>
>>> Hi Aaditaya,
>>>
>>> I don’t think that I’ve ever seen anyone have this problem before. We build 
>>> the expand_instantiations binary, and its supposed to be used when 
>>> expanding files in which we define various combinations of template 
>>> parameters to instantiate templates within the library. If you’re 
>>> interested, you can read more about this here
>>> https://dealii.org/current/doxygen/deal.II/CodingConventions.html
>>> under the "Instantiation of templated functions" section.
>>>
>>> I’m not at all sure what’s gone wrong, but what might be happening is that 
>>> by building in parallel with so many processes you somehow manage to get to 
>>> an object that requires some template parameter expansions before this 
>>> expand_instantiations binary has finished building. Perhaps you can try 
>>> building in serial (or with fewer process) for a little bit, and then 
>>> cancel once you see that you’re definitely at a point where the main 
>>> library object modules are being compiled.
>>>
>>> Perhaps there’s something more that we can do from our side if this is 
>>> indeed the cause of the problem, but that would be a question for Matthias 
>>> (who manages our CMake configuration) to answer. I’m not sure if we can 
>>> somehow delay all other tasks until expand_instantiations binary has been 
>>> built.
>>>
>>> I hope that this helps you to resolve the issue.
>>>
>>> Best,
>>> Jean-Paul
>>>
>>>
>>> On 20 Aug 2020, at 16:16, Aaditya Lakshmanan  wrote:
>>>
>>> Hi Everyone,
>>>
>>> I have been trying to install deal.ii on NERSC Cori cluster 
>>> for use on the KNL compute nodes using the following procedure :
>>>
>>>
>>>
>>> Clone and setup :
>>>
>>> git clone 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-21 Thread Aaditya Lakshmanan
Hi Jean-Paul,
   I cleaned the previous installation, deleted all the files generated in 
the build directory and attempted a fresh build process as follows : 

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 successfully after which I tried installing deal.ii via

make -j 4 install 

which exited with the following error(just as before) :

[ 40%] Building CXX object 
bundled/muparser_v2_2_4/CMakeFiles/obj_muparser_release.dir/src/muParserTest.cpp.o
[ 40%] Generating data_out_dof_data.inst
/bin/sh: expand_instantiations: command not found
make[2]: *** 
[source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: 
source/numerics/data_out_dof_data.inst] Error 127
make[1]: *** [CMakeFiles/Makefile2:3074: 
source/numerics/CMakeFiles/obj_numerics_inst.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
[ 41%] Built target obj_muparser_debug
[ 41%] Generating fe_abf.inst

In the build/bin directory there is a file expand_instantiations of the 
following type :

expand_instantiations: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), 
dynamically linked, interpreter /lib64/l, 
BuildID[sha1]=3ee25c761ad827a88f618b972735b201bc6a2bbe, for GNU/Linux 
3.2.0, with debug_info, not stripped

Is that the file you were referring to earlier? I have attached the 
detailed.log file generated in the build directory. Let me know if you need 
any more information from me. Thank you for your help.

Best,
Aaditya

On Friday, August 21, 2020 at 2:03:59 PM UTC-4 Jean-Paul Pelteret wrote:

> Hi Aaditya,
>
> Great, let us know if that works for you. You should see the 
> expand_instantiations binary appear in the “bin” sub-directory with your 
> build folder. If it still doesn’t appear there, then perhaps you could 
> create a new build directory and then post the configuration and full build 
> logs that come from a fresh build. It could also be that this utility 
> program is failing to build.
>
> Best,
> Jean-Paul
>
> On 21 Aug 2020, at 19:37, Aaditya Lakshmanan  wrote:
>
> Hi Jean-Paul,
>Thank you for your suggestion. I shall try the installation process 
> with fewer processors(perhaps 4) and if even that doesn't work, then I will 
> try it in serial.
>
> Best,
> Aaditya
>
> On Friday, August 21, 2020 at 1:07:54 PM UTC-4 Jean-Paul Pelteret wrote:
>
>> Hi Aaditaya,
>>
>> I don’t think that I’ve ever seen anyone have this problem before. We 
>> build the expand_instantiations binary, and its supposed to be used when 
>> expanding files in which we define various combinations of template 
>> parameters to instantiate templates within the library. If you’re 
>> interested, you can read more about this here
>> https://dealii.org/current/doxygen/deal.II/CodingConventions.html
>> under the "Instantiation of templated functions" section.
>>
>> I’m not at all sure what’s gone wrong, but what might be happening is 
>> that by building in parallel with so many processes you somehow manage to 
>> get to an object that requires some template parameter expansions before 
>> this expand_instantiations binary has finished building. Perhaps you can 
>> try building in serial (or with fewer process) for a little bit, and then 
>> cancel once you see that you’re definitely at a point where the main 
>> library object modules are being compiled.
>>
>> Perhaps there’s something more that we can do from our side if this is 
>> indeed the cause of the problem, but that would be a question for Matthias 
>> (who manages our CMake configuration) to answer. I’m not sure if we can 
>> somehow delay all other tasks until expand_instantiations binary has 
>> been built.
>>
>> I hope that this helps you to resolve the issue.
>>
>> Best,
>> Jean-Paul
>>
>>
>> On 20 Aug 2020, at 16:16, Aaditya Lakshmanan  wrote:
>>
>> Hi Everyone,
>>
>> I have been trying to install deal.ii on NERSC Cori 
>> cluster for use on the KNL compute nodes using the following procedure :
>>  
>>
>> Clone and setup :
>>
>> *git clone --single-branch --branch dealii-9.1 *
>> *https://github.com/dealii/dealii.git* 
>> 
>>
>> *mkdir build*
>>
>> *mkdir dealii_trial*
>>
>> *cd build *
>>  
>>
>> Build and install on an interactive node :
>>
>> *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 completes without any issues after which  
>>  
>>
>> *make -j 32 install* 
>>
>>  eventually yields the following error :
>>
>> 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-21 Thread Jean-Paul Pelteret
Hi Aaditya,

Great, let us know if that works for you. You should see the 
expand_instantiations binary appear in the “bin” sub-directory with your build 
folder. If it still doesn’t appear there, then perhaps you could create a new 
build directory and then post the configuration and full build logs that come 
from a fresh build. It could also be that this utility program is failing to 
build.

Best,
Jean-Paul

> On 21 Aug 2020, at 19:37, Aaditya Lakshmanan  wrote:
> 
> Hi Jean-Paul,
>Thank you for your suggestion. I shall try the installation process with 
> fewer processors(perhaps 4) and if even that doesn't work, then I will try it 
> in serial.
> 
> Best,
> Aaditya
> 
> On Friday, August 21, 2020 at 1:07:54 PM UTC-4 Jean-Paul Pelteret wrote:
> Hi Aaditaya,
> 
> I don’t think that I’ve ever seen anyone have this problem before. We build 
> the expand_instantiations binary, and its supposed to be used when expanding 
> files in which we define various combinations of template parameters to 
> instantiate templates within the library. If you’re interested, you can read 
> more about this here
> https://dealii.org/current/doxygen/deal.II/CodingConventions.html 
> 
> under the "Instantiation of templated functions" section.
> 
> I’m not at all sure what’s gone wrong, but what might be happening is that by 
> building in parallel with so many processes you somehow manage to get to an 
> object that requires some template parameter expansions before this 
> expand_instantiations binary has finished building. Perhaps you can try 
> building in serial (or with fewer process) for a little bit, and then cancel 
> once you see that you’re definitely at a point where the main library object 
> modules are being compiled.
> 
> Perhaps there’s something more that we can do from our side if this is indeed 
> the cause of the problem, but that would be a question for Matthias (who 
> manages our CMake configuration) to answer. I’m not sure if we can somehow 
> delay all other tasks until expand_instantiations binary has been built.
> 
> I hope that this helps you to resolve the issue.
> 
> Best,
> Jean-Paul
> 
> 
> 
>> On 20 Aug 2020, at 16:16, Aaditya Lakshmanan > > wrote:
>> 
> 
>> Hi Everyone,
>> 
>> I have been trying to install deal.ii on NERSC Cori cluster 
>> for use on the KNL compute nodes using the following procedure :
>> 
>>  
>> Clone and setup :
>> 
>> git clone --single-branch --branch dealii-9.1 
>> https://github.com/dealii/dealii.git 
>> mkdir build
>> 
>> mkdir dealii_trial
>> 
>> cd build 
>> 
>>  
>> Build and install on an interactive node :
>> 
>> 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 completes without any issues after which  
>> 
>>  
>> make -j 32 install 
>> 
>>  eventually yields the following error :
>> 
>> --
>> 
>> [ 27%] Building CXX object 
>> bundled/umfpack/AMD/Source/CMakeFiles/obj_amd_long_debug.dir/amd_defaults.cc.o
>> 
>> /bin/sh: expand_instantiations: command not found
>> 
>> make[2]: *** 
>> [source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: 
>> source/numerics/data_out_dof_data.inst] Error 127
>> 
>> make[2]: *** Waiting for unfinished jobs
>> 
>> ---
>> 
>> Details on procedure before cloning deal.ii are included below :
>> 
>> (i) I first loaded the necessary modules so that module list displayed 
>> 
>> Currently Loaded Modulefiles:
>> 
>>   1) modules/3.2.11.4  
>>16) rca/2.2.20-7.0.1.1_4.46__g8e3fb5b.ari
>> 
>>   2) altd/2.0
>>  17) atp/2.1.3
>> 
>>   3) darshan/3.1.7  
>> 18) PrgEnv-intel/6.0.5
>> 
>>   4) intel/19.0.3.199    
>> 19) craype-mic-knl
>> 
>>   5) craype-network-aries  20) 
>> cray-mpich/7.7.14
>> 
>>   6) craype/2.6.2
>>  21) craype-hugepages2M
>> 
>>   7) udreg/2.3.2-7.0.1.1_3.31__g8175d3d.ari   22) valgrind/3.15.0
>> 
>>   8) ugni/6.0.14.0-7.0.1.1_7.33__ge78e5b0.ari 23) zlib/1.2.11
>> 
>>   9) pmi/5.0.14  
>>24) metis/5.1.0
>> 
>>  10) dmapp/7.1.1-7.0.1.1_4.48__g38cf134.ari   25) parmetis/4.0.3
>> 
>>  11) 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-21 Thread Aaditya Lakshmanan
Hi Jean-Paul,
   Thank you for your suggestion. I shall try the installation process with 
fewer processors(perhaps 4) and if even that doesn't work, then I will try 
it in serial.

Best,
Aaditya

On Friday, August 21, 2020 at 1:07:54 PM UTC-4 Jean-Paul Pelteret wrote:

> Hi Aaditaya,
>
> I don’t think that I’ve ever seen anyone have this problem before. We 
> build the expand_instantiations binary, and its supposed to be used when 
> expanding files in which we define various combinations of template 
> parameters to instantiate templates within the library. If you’re 
> interested, you can read more about this here
> https://dealii.org/current/doxygen/deal.II/CodingConventions.html
> under the "Instantiation of templated functions" section.
>
> I’m not at all sure what’s gone wrong, but what might be happening is that 
> by building in parallel with so many processes you somehow manage to get to 
> an object that requires some template parameter expansions before this 
> expand_instantiations binary has finished building. Perhaps you can try 
> building in serial (or with fewer process) for a little bit, and then 
> cancel once you see that you’re definitely at a point where the main 
> library object modules are being compiled.
>
> Perhaps there’s something more that we can do from our side if this is 
> indeed the cause of the problem, but that would be a question for Matthias 
> (who manages our CMake configuration) to answer. I’m not sure if we can 
> somehow delay all other tasks until expand_instantiations binary has been 
> built.
>
> I hope that this helps you to resolve the issue.
>
> Best,
> Jean-Paul
>
>
> On 20 Aug 2020, at 16:16, Aaditya Lakshmanan  wrote:
>
> Hi Everyone,
>
> I have been trying to install deal.ii on NERSC Cori 
> cluster for use on the KNL compute nodes using the following procedure :
>  
>
> Clone and setup :
>
> *git clone --single-branch --branch dealii-9.1 *
> *https://github.com/dealii/dealii.git* 
> 
>
> *mkdir build*
>
> *mkdir dealii_trial*
>
> *cd build *
>  
>
> Build and install on an interactive node :
>
> *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 completes without any issues after which  
>  
>
> *make -j 32 install* 
>
>  eventually yields the following error :
>
> --
>
> [ 27%] Building CXX object 
> bundled/umfpack/AMD/Source/CMakeFiles/obj_amd_long_debug.dir/amd_defaults.cc.o
>
> /bin/sh: expand_instantiations: command not found
>
> make[2]: *** 
> [source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: 
> source/numerics/data_out_dof_data.inst] Error 127
>
> make[2]: *** Waiting for unfinished jobs
>
> ---
>
> Details on procedure before cloning deal.ii are included below :
>
> (i) I first loaded the necessary modules so that *module list* displayed 
>
> Currently Loaded Modulefiles:
>
>   1) modules/3.2.11.416) 
> rca/2.2.20-7.0.1.1_4.46__g8e3fb5b.ari
>
>   2) 
> altd/2.0 
> 17) 
> atp/2.1.3
>
>   3) 
> darshan/3.1.7  18) 
> PrgEnv-intel/6.0.5
>
>   4) intel/19.0.3.199   
> 19) 
> craype-mic-knl
>
>   5) craype-network-aries  20) 
> cray-mpich/7.7.14
>
>   6) 
> craype/2.6.2 21) 
> craype-hugepages2M
>
>   7) udreg/2.3.2-7.0.1.1_3.31__g8175d3d.ari   22) valgrind/3.15.0
>
>   8) ugni/6.0.14.0-7.0.1.1_7.33__ge78e5b0.ari 23) zlib/1.2.11
>
>   9) 
> pmi/5.0.14 
> 24) 
> metis/5.1.0
>
>  10) dmapp/7.1.1-7.0.1.1_4.48__g38cf134.ari   25) parmetis/4.0.3
>
>  11) gni-headers/5.0.12.0-7.0.1.1_6.28__g3b1768f.ari  26) 
> superlu-dist/6.1.1
>
>  12) xpmem/2.2.20-7.0.1.1_4.10__g0475745.ari27) hypre/2.15.1
>
>  13) job/2.2.4-7.0.1.1_3.36__g36b56f4.ari   28) 
> cmake/3.14.4
>
>  14) dvs/2.12_2.2.156-7.0.1.1_8.9__g5aab709e 29) cray-hdf5/
> 1.10.2.0
>
>  15) alps/6.6.58-7.0.1.1_6.4__g437d88db.ari  30) 
> petsc-real-64/3.11.2
>  
>
> (ii) Set environment variables for dynamic linking 
>
> *export XTPE_LINK_TYPE=dynamic*
>
> *export CRAYPE_LINK_TYPE=dynamic*
>  
>
> (iii) p4est installation
>
> *./configure --prefix=/global/project/projectdirs/m2360/packagesCPFE/p4est 
> --host=x86_64 

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-21 Thread Jean-Paul Pelteret
Hi Aaditaya,

I don’t think that I’ve ever seen anyone have this problem before. We build the 
expand_instantiations binary, and its supposed to be used when expanding files 
in which we define various combinations of template parameters to instantiate 
templates within the library. If you’re interested, you can read more about 
this here
https://dealii.org/current/doxygen/deal.II/CodingConventions.html 

under the "Instantiation of templated functions" section.

I’m not at all sure what’s gone wrong, but what might be happening is that by 
building in parallel with so many processes you somehow manage to get to an 
object that requires some template parameter expansions before this 
expand_instantiations binary has finished building. Perhaps you can try 
building in serial (or with fewer process) for a little bit, and then cancel 
once you see that you’re definitely at a point where the main library object 
modules are being compiled.

Perhaps there’s something more that we can do from our side if this is indeed 
the cause of the problem, but that would be a question for Matthias (who 
manages our CMake configuration) to answer. I’m not sure if we can somehow 
delay all other tasks until expand_instantiations binary has been built.

I hope that this helps you to resolve the issue.

Best,
Jean-Paul


> On 20 Aug 2020, at 16:16, Aaditya Lakshmanan  wrote:
> 
> Hi Everyone,
> 
> I have been trying to install deal.ii on NERSC Cori cluster 
> for use on the KNL compute nodes using the following procedure :
> 
>  
> Clone and setup :
> 
> git clone --single-branch --branch dealii-9.1 
> https://github.com/dealii/dealii.git 
> mkdir build
> 
> mkdir dealii_trial
> 
> cd build 
> 
>  
> Build and install on an interactive node :
> 
> 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 completes without any issues after which  
> 
>  
> make -j 32 install 
> 
>  eventually yields the following error :
> 
> --
> 
> [ 27%] Building CXX object 
> bundled/umfpack/AMD/Source/CMakeFiles/obj_amd_long_debug.dir/amd_defaults.cc.o
> 
> /bin/sh: expand_instantiations: command not found
> 
> make[2]: *** [source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: 
> source/numerics/data_out_dof_data.inst] Error 127
> 
> make[2]: *** Waiting for unfinished jobs
> 
> ---
> 
> Details on procedure before cloning deal.ii are included below :
> 
> (i) I first loaded the necessary modules so that module list displayed 
> 
> Currently Loaded Modulefiles:
> 
>   1) modules/3.2.11.416) 
> rca/2.2.20-7.0.1.1_4.46__g8e3fb5b.ari
> 
>   2) altd/2.0 
> 17) atp/2.1.3
> 
>   3) darshan/3.1.7  
> 18) PrgEnv-intel/6.0.5
> 
>   4) intel/19.0.3.199   
> 19) craype-mic-knl
> 
>   5) craype-network-aries  20) 
> cray-mpich/7.7.14
> 
>   6) craype/2.6.2 
> 21) craype-hugepages2M
> 
>   7) udreg/2.3.2-7.0.1.1_3.31__g8175d3d.ari   22) valgrind/3.15.0
> 
>   8) ugni/6.0.14.0-7.0.1.1_7.33__ge78e5b0.ari 23) zlib/1.2.11
> 
>   9) pmi/5.0.14   
>   24) metis/5.1.0
> 
>  10) dmapp/7.1.1-7.0.1.1_4.48__g38cf134.ari   25) parmetis/4.0.3
> 
>  11) gni-headers/5.0.12.0-7.0.1.1_6.28__g3b1768f.ari  26) superlu-dist/6.1.1
> 
>  12) xpmem/2.2.20-7.0.1.1_4.10__g0475745.ari27) hypre/2.15.1
> 
>  13) job/2.2.4-7.0.1.1_3.36__g36b56f4.ari   28) 
> cmake/3.14.4
> 
>  14) dvs/2.12_2.2.156-7.0.1.1_8.9__g5aab709e 29) 
> cray-hdf5/1.10.2.0
> 
>  15) alps/6.6.58-7.0.1.1_6.4__g437d88db.ari  30) 
> petsc-real-64/3.11.2
> 
>  
> (ii) Set environment variables for dynamic linking 
> 
> export XTPE_LINK_TYPE=dynamic
> 
> export CRAYPE_LINK_TYPE=dynamic
> 
>  
> (iii) p4est installation
> 
> ./configure --prefix=/global/project/projectdirs/m2360/packagesCPFE/p4est 
> --host=x86_64 --enable-vtk-zlib=yes  --enable-mpi=yes F77=ftn FC=ftn CC=cc 
> CXX=CC
> 
> make -j 32
> 
> make -j 32 install 
> 
> export P4EST_DIR=/global/project/projectdirs/m2360/packagesCPFE/p4est
> 
> I did initially submit a ticket on NERSC support for assistance with the 
> installation process 

Re: [deal.II] Deal.ii installation

2020-06-09 Thread Jean-Paul Pelteret
Dear Prasad,

I’m glad to hear that you solved your problem. I must say, though, that the 
problem and the solution only seems to me to be tangentially related.  Although 
neither you, I, nor probably anyone else could have guessed from the cryptic 
and nondescript error message, you were probably missing some critical core 
package required to build the library. Many of these dependencies would be 
installed via

sudo apt-get install build-essential  

but it could be that something else is required. Here, for example, is a list 
of the packages assumed to be installed when building deal.II using Candi.

https://github.com/dealii/candi/blob/master/deal.II-toolchain/platforms/supported/ubuntu20.platform#L6-L10

Note through that many of these packages would only be required by the 
dependencies (e.g. Trilinos). The key one there is, again, probably 
build-essential . But this is just speculation - I currently don’t have an 
Ubuntu installation with to test my suspicion. But I thought I’d just share my 
thoughts in case someone else hits the same problem and spots this thread while 
looking for a solution.

Best,
Jean-Paul

> On 03 Jun 2020, at 19:24, Prasad Adhav  wrote:
> 
> I was able to solve the issue by installing trilinos-all-dev.
> 
> ~$ sudo apt-get update -y
> ~$ sudo apt-get install -y trilinos-all-dev
> 
> Download Deal.ii
> Moved it to bin
> 
> ~/bin$ tar -xvf deal.II-9.1.1.tar.gz
> ~/bin/dealii-9.1.1$ mkdir build
> ~/bin/dealii-9.1.1$ cd build
> ~/bin/dealii-9.1.1/build$ cmake 
> -DCMAKE_INSTALL_PREFIX=/home/prasad/bin/deal.II ..
> ~/bin/dealii-9.1.1/build$ make install
> ~/bin/dealii-9.1.1/build$ make test
> 
> prasad@XDEM-laptop:~/bin/dealii-9.1.1/build$ make test 
> Scanning dependencies of target test 
> Running quicktests... 
> Test project /home/prasad/bin/dealii-9.1.1/build/tests/quick_tests 
>Start 1: step.debug 
>Start 2: step.release 
>Start 3: affinity.debug 
>Start 4: tbb.debug 
>Start 5: lapack.debug 
>Start 6: umfpack.debug 
>Start 7: boost_zlib.debug 
>Start 8: gmsh.debug 
> 1/8 Test #5: lapack.debug .   Passed   34.73 sec 
> 2/8 Test #4: tbb.debug    Passed   38.34 sec 
> 3/8 Test #8: gmsh.debug ...   Passed   44.55 sec 
> 4/8 Test #7: boost_zlib.debug .   Passed   44.97 sec 
> 5/8 Test #3: affinity.debug ...   Passed   44.98 sec 
> 6/8 Test #6: umfpack.debug    Passed   48.18 sec 
> 7/8 Test #2: step.release .   Passed   52.11 sec 
> 8/8 Test #1: step.debug ...   Passed   54.85 sec 
> 
> 100% tests passed, 0 tests failed out of 8 
> 
> Total Test time (real) =  54.85 sec 
> Built target test
> 
> 
> On Monday, April 27, 2020 at 11:27:31 AM UTC+2, Prasad Adhav wrote:
> Hello,
> 
> I am trying to install deal.ii for the first time.
> I followed the instructions on the readme 
> page(https://www.dealii.org/current/readme.html 
> )
> 
> I use the following for cmake and it worked fine:
> 
> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ cmake 
> -DCMAKE_INSTALL_PREFIX=/home/
> prasad/Downloads/dealii-9.1.1/dealii_install/ ..
> 
> Then I tried to do `make`, `make info` and `make install`, I get a similar 
> error as follows:
> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make info 
> make: *** No rule to make target 'info'.  Stop.
> 
> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make install 
> make: *** No rule to make target 'install'.  Stop.
> 
> I apologize if this was already posted, in my search I did not find any 
> questions similar to this.
> Can anyone help with this?
> Thank you.
> 
> 
> 
> 
> -- 
> 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 
> 
> --- 
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> "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/8ff0c50c-0433-4ed3-950b-fb2b1f754f96%40googlegroups.com
>  
> .

-- 
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Re: [deal.II] Deal.ii installation

2020-04-27 Thread Wolfgang Bangerth

On 4/27/20 3:27 AM, Prasad Adhav wrote:


prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ cmake 
-DCMAKE_INSTALL_PREFIX=/home/

prasad/Downloads/dealii-9.1.1/dealii_install/ ..

Then I tried to do `make`, `make info` and `make install`, I get a similar 
error as follows:

prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make info
make: *** No rule to make target 'info'.  Stop.


In your build directory, is there actually a 'Makefile' file? My suspicion is 
that cmake did not, in fact, succeed...


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 on cray XC50 giving MPI_VERSION=0.0

2020-02-06 Thread Wolfgang Bangerth

On 2/6/20 6:18 AM, Daniel Arndt wrote:


You can probably tell better than any of us if this works. Just try. It might 
quite well be that the compiler doesn't need any extra flags for MPI. Also, it 
looks like the MPI version could not be detected. This implies that the 
library doesn't use newer features but should still work. If you know to which 
standard the MPI installation is conforming, you could try to set it via


cmake -DMPI_VERSION=...

yourself.
If there any more problems, feel free to tell us.


But separately, we try to obtain the MPI version from the file mpi.h via the 
following cmake code in cmake/modules/FindMPI.h:


DEAL_II_FIND_FILE(MPI_MPI_H
  NAMES mpi.h
  HINTS ${MPI_CXX_INCLUDE_PATH} ${MPI_C_INCLUDE_PATH}
  )
IF(NOT MPI_MPI_H MATCHES "-NOTFOUND" AND NOT DEFINED MPI_VERSION)
  FILE(STRINGS "${MPI_MPI_H}" MPI_VERSION_MAJOR_STRING
REGEX "#define.*MPI_VERSION")
  STRING(REGEX REPLACE "^.*MPI_VERSION[ ]+([0-9]+).*" "\\1"
MPI_VERSION_MAJOR "${MPI_VERSION_MAJOR_STRING}"
)
  FILE(STRINGS ${MPI_MPI_H} MPI_VERSION_MINOR_STRING
REGEX "#define.*MPI_SUBVERSION")
  STRING(REGEX REPLACE "^.*MPI_SUBVERSION[ ]+([0-9]+).*" "\\1"
MPI_VERSION_MINOR "${MPI_VERSION_MINOR_STRING}"
)
  SET(MPI_VERSION "${MPI_VERSION_MAJOR}.${MPI_VERSION_MINOR}")
ENDIF()


It would be interesting to see why that files. Can you try and find out which 
mpi.h on your system is being used, and attach it to a reply?


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 on cray XC50 giving MPI_VERSION=0.0

2020-02-06 Thread Daniel Arndt
Vachan,

You can probably tell better than any of us if this works. Just try. It
might quite well be that the compiler doesn't need any extra flags for MPI.
Also, it looks like the MPI version could not be detected. This implies
that the library doesn't use newer features but should still work. If you
know to which standard the MPI installation is conforming, you could try to
set it via

cmake -DMPI_VERSION=...

yourself.
If there any more problems, feel free to tell us.

Best,
Daniel

On Thu, Feb 6, 2020, 1:10 AM vachan potluri 
wrote:

> Hello,
>
> I am trying to install deal.II on a cray XC50 supercomputer.
>
> cmake -DCMAKE_INSTALL_PREFIX=~/bin/dealii-9.1.1 \
> -DPREFIX_PATH=/opt/cray/pe \
> -DCMAKE_CXX_COMPILER=/opt/cray/pe/craype/2.5.13/bin/CC \
> -DWITH_MPI=ON \
> -DWITH_PETSC=OFF -DPETSC_DIR=$PETSC_DIR -DPETSC_ARCH=$PETSC_ARCH \
> -DWITH_P4EST=ON -DP4EST_DIR=~/bin/p4est-2.2 \
> ~/source/dealii-9.1.1
>
> I have attached detailed.log and summary.log. Although the configuring
> exits without errors, I can see in detailed.log that MPI_VERSION was not
> detected correctly. The compilers were correctly detected. All other
> variables are just blanks. The relevant snippet of detailed.log is as
> follows:
>
> #DEAL_II_WITH_MPI set up with external dependencies
> #MPI_VERSION = 0.0
> #MPI_C_COMPILER = /opt/cray/pe/craype/2.5.13/bin/cc
> #MPI_CXX_COMPILER = /opt/cray/pe/craype/2.5.13/bin/CC
> #MPI_Fortran_COMPILER = /opt/cray/pe/craype/2.5.13/bin/ftn
> #MPI_CXX_FLAGS =
> #MPI_LINKER_FLAGS =
> #MPI_INCLUDE_DIRS =
> #MPI_USER_INCLUDE_DIRS =
> #MPI_LIBRARIES =
>
> Is this an issue? How to fix this? I had loaded cray-mpich module before
> invoking cmake and switched PrgEnv-cray with PrgEnv-gnu.
>
> --
> 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
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> 
> .
>

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Re: [deal.II] Deal.ii installation problem:- Step 40 runtime error

2018-01-23 Thread RAJAT ARORA
Hello Professor,

Thanks for the reply. 
I had been struggling with this issue for 5 days now. I raised the ticket 
on XSEDE forum on 18th Jan.
The technical team was expecting everything was fine from their side and 
advised me to reinstall with some different modules loaded. They were also 
expecting mixing of different mpi components.

I actually tried every possible combination (over 20) of modules. When 
nothing worked, I finally decided that to seek help from this forum. I was 
hesitating at first as I was sure that this is not the problem with library 
or its installation but rather it is the problem with the system. I needed 
some guidance to prove this thing.

However, I finally received an email yesterday (after posting this), that 
they made some security update on the system last week which caused the 
issue.  After the change was corrected by them, everything works fine just 
using candi.

Thanks a lot for the help. I really appreciate it.

I am still posting the answers to the questions you asked.

1. It always used to happen at a different position when run with different 
processors on a single node.

2. Even using multiple nodes was giving this error.










On Monday, January 22, 2018 at 11:09:41 PM UTC-5, Wolfgang Bangerth wrote:
>
> On 01/22/2018 08:48 AM, RAJAT ARORA wrote: 
> > 
> > Running with PETSc on 2 MPI rank(s)... 
> > Cycle 0: 
> > Number of active cells:   1024 
> > Number of degrees of freedom: 4225 
> > Solved in 10 iterations. 
> > 
> > 
> > 
> +-+++ 
> > | Total wallclock time elapsed since start| 0.222s |   
>  | 
> > | ||   
>  | 
> > | Section | no. calls |  wall time | % of total 
> | 
> > 
> +-+---+++ 
> > | assembly| 1 | 0.026s |12% 
> | 
> > | output  | 1 |0.0448s |20% 
> | 
> > | setup   | 1 |0.0599s |27% 
> | 
> > | solve   | 1 |0.0176s |   7.9% 
> | 
> > 
> +-+---+++ 
> > 
> > 
> > Cycle 1: 
> > Number of active cells:   1960 
> > Number of degrees of freedom: 8421 
> > r001.pvt.bridges.psc.edu.27927Assertion failure at 
> > 
> /nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.3.3/ptl_am/ptl.c:152:
>  
>
> > nbytes == req->recv_msglen 
> > r001.pvt.bridges.psc.edu.27927step-40: Reading from remote process' 
> memory 
> > failed. Disabling CMA support 
> > [r001:27927] *** Process received signal *** 
>
> These error messages suggest that the first cycle actually worked. So your 
> MPI 
> installation is not completely broken apparently. 
>
> Is the error message reproducible? Is it always in the same place and with 
> the 
> same message? When you run two processes, are they on separate machines or 
> on 
> the same one? 
>
> 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 problem:- Step 40 runtime error

2018-01-22 Thread Wolfgang Bangerth

On 01/22/2018 08:48 AM, RAJAT ARORA wrote:


Running with PETSc on 2 MPI rank(s)...
Cycle 0:
Number of active cells:   1024
Number of degrees of freedom: 4225
Solved in 10 iterations.


+-+++
| Total wallclock time elapsed since start| 0.222s ||
| |||
| Section | no. calls |  wall time | % of total |
+-+---+++
| assembly| 1 | 0.026s |12% |
| output  | 1 |0.0448s |20% |
| setup   | 1 |0.0599s |27% |
| solve   | 1 |0.0176s |   7.9% |
+-+---+++


Cycle 1:
Number of active cells:   1960
Number of degrees of freedom: 8421
r001.pvt.bridges.psc.edu.27927Assertion failure at 
/nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.3.3/ptl_am/ptl.c:152: 
nbytes == req->recv_msglen
r001.pvt.bridges.psc.edu.27927step-40: Reading from remote process' memory 
failed. Disabling CMA support

[r001:27927] *** Process received signal ***


These error messages suggest that the first cycle actually worked. So your MPI 
installation is not completely broken apparently.


Is the error message reproducible? Is it always in the same place and with the 
same message? When you run two processes, are they on separate machines or on 
the same one?


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 Error

2017-04-17 Thread RAJAT ARORA
Hello Timo,

Thanks for the reply. I didn't know about the compilation problems with 
older intel compilers.

Yes, this problem was occurring with intel 2013 update 5 and openmpi 1.7.2

The problem is resolved when I switch to intel 2015 compiler and 
openmpi 1.8.4.

This could be because of the compiler compatibility issue as you mentioned. 

Thanks again.

On Sunday, April 16, 2017 at 6:02:47 PM UTC-4, Timo Heister wrote:
>
> Rajat, 
>
> first, is there a reason you are using deal.II 8.3.0, which is by now 
> to big releases behind? 
> Second, can is there a more modern MPI and compiler you can try? We 
> have had many problems with intel compilers in the past, so I would 
> try a gcc with mpich or openmpi unless you are sure in what you are 
> doing. 
>
> On Sat, Apr 15, 2017 at 5:19 PM, RAJAT ARORA  > wrote: 
> > Hello Everyone, 
> > 
> > I am trying to install deal.ii on Minnesota supercomputing institute 
> using 
> > openmpi compiled with intel. 
> > 
> > However, I am getting several errors during installation. 
> > 
> > I am attaching the install.log file (output of deal.ii installation) 
> since 
> > the errors are huge. 
> > 
> > It starts from line 1878 when the installation reaches 92% during the 
> > compilation of file mapping_fe_field.cc. 
> > 
> > Please help me with the installation. 
> > 
> > Thanks. 
> > 
> > 
> > 
> > -- 
> > The deal.II project is located at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0=SS_oJV8kSW8xkwLez-eSx8Xf5agwsaX8_Zm413D7izU=
>  
> > For mailing list/forum options, see 
> > 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0=HYTlTvyBdQWDnTjTrRwi2512DbH-prGRo3eLZECzkhU=
>  
> > --- 
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> Groups 
> > "deal.II User Group" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to dealii+un...@googlegroups.com . 
> > For more options, visit 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0=StK1bh8JvaISuWUcq6kQSHXJOkyulCANz3pb0m7Ge_0=
>  
> . 
>
>
>
> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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Re: [deal.II] Deal.ii installation Error

2017-04-16 Thread Timo Heister
Rajat,

first, is there a reason you are using deal.II 8.3.0, which is by now
to big releases behind?
Second, can is there a more modern MPI and compiler you can try? We
have had many problems with intel compilers in the past, so I would
try a gcc with mpich or openmpi unless you are sure in what you are
doing.

On Sat, Apr 15, 2017 at 5:19 PM, RAJAT ARORA  wrote:
> Hello Everyone,
>
> I am trying to install deal.ii on Minnesota supercomputing institute using
> openmpi compiled with intel.
>
> However, I am getting several errors during installation.
>
> I am attaching the install.log file (output of deal.ii installation) since
> the errors are huge.
>
> It starts from line 1878 when the installation reaches 92% during the
> compilation of file mapping_fe_field.cc.
>
> Please help me with the installation.
>
> Thanks.
>
>
>
> --
> The deal.II project is located at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=ZzAFG_s-rwwy08oT7yXypuWGWX173CTEdDNsG-y3Yu0=SS_oJV8kSW8xkwLez-eSx8Xf5agwsaX8_Zm413D7izU=
>  
> For mailing list/forum options, see
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>  
> ---
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>  .



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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