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

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

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

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

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 .

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

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

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

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

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

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 >

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

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

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

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

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

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

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.

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

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

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

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

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

2020-08-20 Thread Aaditya Lakshmanan
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*

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

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:

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

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

[deal.II] deal.II installation on cray XC50 giving MPI_VERSION=0.0

2020-02-05 Thread vachan potluri
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

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

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

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

2018-01-22 Thread RAJAT ARORA
Hello all, I recently installed deal.ii using candi but after everything successfully finishes, I am not able to run step-40 on more than 1 processor. For, 1 processor it runs fine. To install everything, I used candi and and loaded following modules. 1) psc_path/1.1 2) slurm/17.02.5

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

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