get errors when installing dealii on openSUSE Leap 42.1 by using candi

[Roc Wang]

Hello,

   I am trying to install dealii on openSUSE Leap 42.1 by using candi downloaded from https://github.com/dealii/candi?files=1. However, I got error when it compiled zlib-1.2.8. The error info is like as:

Fetching zlib 1.2.8
Verifying zlib-1.2.8.tar.gz
zlib-1.2.8.tar.gz: OK
zlib-1.2.8.tar.gz already downloaded and verified.
Unpacking zlib-1.2.8.tar.gz
Building zlib 1.2.8
Compiler error reporting is too harsh for ./configure (perhaps remove -Werror).
** ./configure aborting.
Failure with exit status: 1
Exit message: There was a problem building zlib 1.2.8.

   I tried to install zlib in openSUSE from repository, but, libz1 providing zlib was found. The info is like:

Loading repository data...
Reading installed packages...
'zlib' not found in package names. Trying capabilities.
'libz1' providing 'zlib' is already installed.
Resolving package dependencies…

                    

Nothing to do.

Should I and How to remove the -Werror flag in ./configure? Please someone help me on this? Thanks!!

[Bruno Turcksin]

Hi

On Thursday, June 9, 2016 at 4:49:30 AM UTC-4, Roc Wang wrote:

   I tried to install zlib in openSUSE from repository, but, libz1 providing zlib was found. The info is like:

Loading repository data...
Reading installed packages...
'zlib' not found in package names. Trying capabilities.
'libz1' providing 'zlib' is already installed.
Resolving package dependencies…

                    

Nothing to do.

If I remember correctly, candi tries to install zlib only when your platform is a generic linux_cluster because it cannot guarantee that zlib was installed by the package manager. The different supported platforms are mainly there to ensure that all the packages that should be installed by the package manager were installed.  You should be able to use candi using opensuse13.platform This won't trigger the build of zlib.

Best,

Bruno

[Tuanny Cajuhi]

Dear all,

I am trying to install dealii on a cluster using

./candi.sh --platform=./deal.II-toolchain/platforms/supported/linux_cluster.platform

and I get the same error as reported here:

Building zlib 1.2.8 
Compiler error reporting is too harsh for ./configure (perhaps remove -Werror). 
** ./configure aborting. 
Failure with exit status: 1 
Exit message: There was a problem building zlib 1.2.8.

Could you please help me? 

Thank you!

 
Best regards,
Tuanny 

[Bruno Turcksin]

Tuanny,

we need to see the log file to know why it is failing. There is also a
good chane that zlib is already installed on the cluster so you could
comment once:zlib (line 21) in
candi/deal.II-toolchain/platforms/supported/linux_cluster.platform and
try again.

Best,

Bruno

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[Uwe Köcher]

Dear Tuanny,

if you have zlib already installed on your system, remove the line with zlib from the linux_cluster.platform,

it is located in ./candi/deal.II-toolchain/platforms/supported/linux_cluster.platform.

If you not have zlib installed, you should try to modify the package file of zlib. This file is

located at ./candi/deal.II-toolchain/packages/zlib.package

add the line with CFLAG as

    cp -rf ${UNPACK_PATH}/${EXTRACTSTO}/* .
    CFLAGS="$CFLAGS -Wno-error"
    ./configure --prefix=${INSTALL_PATH}

and then run candi again.

Kind regards

  Uwe

[Tuanny Cajuhi]

Dear Bruno, dear Uwe,

thank you for the hints.

I checked and zlib (whereis zlib) is indeed available in the cluster. I first deleted the line in *platform, then I tried to run candi. I got a similar error for the next library in the *platform file: bzip2. I proceeded the same way and deleted bzip2 (also available).

I checked and did not find boost. By running candi again, I got:

Failure with exit status: 1

Exit message: There was a problem building boost 1_63_0.

(attached you can find all the messages from the terminal)

I don't know if it is important to mention, but I could not access the mirror (https://cecas.clemson.edu/dealii/mirror/) to download the packages at first (before getting the first problem with the zlib). Then I downloaded them myself and changed the address of the mirror to my local files in candi.cfg.  

Is there another way to try this installation or am I forgetting something?
Thanks.

Best, 
Tuanny 

[Bruno Turcksin]

Tuanny,

2017-06-01 3:53 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> Failure with exit status: 1
> Exit message: There was a problem building boost 1_63_0.
> (attached you can find all the messages from the terminal)

The problem is this "libs/python/src/numpy/dtype.cpp:61: error:
‘NPY_FLOAT16’ was not declared in this scope" There is a problem when
compiling boost python. You probably have a very old version of python
on your cluster. You don't need boost python so you should be able to
use the version of boost installed by candi. You can also change the
configuration yourself so boost doesn't even try to compile boost
python. I want to point out that boost also throw this warning "MPI
auto-detection failed: unknown wrapper compiler mpic++" This is kind
of strange so make sure that you have loaded the right mpi module.

> Is there another way to try this installation or am I forgetting something?

You can use spack
https://github.com/dealii/dealii/wiki/deal.II-in-Spack but you need to
make sure that you are using the mpi from your cluster. You can also
install everything by hand...

Best,

Bruno

[Tuanny Cajuhi]

Hi Bruno,

I was able to build boost after loading the module to update Python. Thanks a lot for the hint!

My next issue is p4est...

Unpacking p4est-2.0.tar.gz

Building p4est 2.0

CFLAGS_FAST: -O2

CFLAGS_DEBUG: -O0 -g

This script tries configure and build the p4est library.

Build FAST: /home/h/niitcaju/deal.ii-candi/tmp/build/p4est-2.0/FAST

Build DEBUG: /home/h/niitcaju/deal.ii-candi/tmp/build/p4est-2.0/DEBUG

Install FAST: /home/h/niitcaju/deal.ii-candi/p4est-2.0/FAST

Install DEBUG: /home/h/niitcaju/deal.ii-candi/p4est-2.0/DEBUG

Checking environment: CFLAGS P4EST_CFLAGS_FAST P4EST_CFLAGS_DEBUG

See output in files .../config.output and .../make.output

Build FAST version in /home/h/niitcaju/deal.ii-candi/tmp/build/p4est-2.0/FAST

configure: error: in `/home/h/niitcaju/deal.ii-candi/tmp/build/p4est-2.0/FAST':

configure: error: Fortran 77 compiler cannot create executables

See `config.log' for more details

Best regards,
Tuanny

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Tuanny Cajuhi

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+49 176 323 191 85

[Tuanny Cajuhi]

...

and the 2 lines with 'error' in the config.log:

configure:4404: error: in `/home/h/niitcaju/deal.ii-candi/tmp/build/p4est-2.0/FAST':

configure:4406: error: Fortran 77 compiler cannot create executables

[Bruno Turcksin]

Tuanny,

2017-06-01 9:56 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> My next issue is p4est...

:-(

> Build FAST version in /home/h/niitcaju/deal.ii-candi/tmp/build/p4est-2.0/FAST
> configure: error: in `/home/h/niitcaju/deal.ii-candi/tmp/build/p4est-2.0/FAST':
> configure: error: Fortran 77 compiler cannot create executables
> See `config.log' for more details

Are you using the same version of gfortran and gcc? Can you send the
whole config.log. I need to see what's the environment that p4est is
using.

Thanks

Bruno

[Tuanny Cajuhi]

Hi Bruno,

thank you. 

Are you using the same version of gfortran and gcc? Can you send the
whole config.log. I need to see what's the environment that p4est is
using.

/opt/gcc/6.2.0/bin/gfortran

/opt/gcc/6.2.0/bin/gcc

​The log is attached. Thank you for the help!

[Bruno Turcksin]

This is the problem "mpif77: command not found" Does mpif77 exist? If
not, does mpif90 exist? If yes try export F77=mpif90

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[Tuanny Cajuhi]

I did not find any of them... :/ 

> dealii+unsubscribe@googlegroups.com.

> For more options, visit https://groups.google.com/d/optout.

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[Bruno Turcksin]

2017-06-01 10:34 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> I did not find any of them... :/

That's very strange how do you compile a mpi program by hand? Do you
have mpic++ ? Are you on a cray?

[Tuanny Cajuhi]

I am on a cray (loaded module cray-mpich/7.5.1) and I don't know how to explicitly call one thing or the other 

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[Bruno Turcksin]

2017-06-01 10:40 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> I am on a cray (loaded module cray-mpich/7.5.1) and I don't know how to
> explicitly call one thing or the other

Oh that explains a lot. Not sure that candi is going to work then.
Cray don't work like other clusters :-/ One big difference is that
they don't have things like mpicxx. Instead, you need to use their own
wrappers. So the problem is that you will need to tell every package
using mpi to look for CC instead of mpicxx (same thing with fortran,
etc). So you have three choices:
1) ask your admin to install deal for you
2) use spack that has support for cray but I don't think anyone has
ever tried to use spack to install deal on a cray.
3) install every package by hand. Which other package do you need? Can
you load a module for everything left but p4est?

[Tuanny Cajuhi]

1) ask your admin to install deal for you

​I asked but it seems to not an option at the moment... 

2) use spack that has support for cray but I don't think anyone has
ever tried to use spack to install deal on a cray.

 

​I tried to install using spack as you suggested in the previous message, but also got stuck. Basically I changed to module load cray-mpich/7.5.1, but then did not come further in (3) because I did not know how to change/what to change in packages. Do you have an idea on what could be done/changed in the packages list? 

 

3) install every package by hand. Which other package do you need? Can
you load a module for everything left but p4est?

 

I would need to install the numdiff, bzip2. Basically the things that the git would do in a more intuitive way :/

Thank you so much for the help.

[Bruno Turcksin]

2017-06-01 11:03 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> I tried to install using spack as you suggested in the previous message, but
> also got stuck. Basically I changed to module load cray-mpich/7.5.1, but
> then did not come further in (3) because I did not know how to change/what
> to change in packages. Do you have an idea on what could be done/changed in
> the packages list?

Sorry I have never used spack on a cray.

> I would need to install the numdiff, bzip2. Basically the things that the
> git would do in a more intuitive way :/

Well you don't need numdiff and you can load bzip2 from a module
right? My question is more do you just need to install p4est and deal
and you can load modules for everything else or do you need to install
your own Trilinos with all its dependencies or a specific version of
petsc. I have installed deal on a cray before and if you just need
p4est and deal, it shouldn't be too bad. Now if you need to install
your own superLU-dist for Trilinos, it's another beast...

[Tuanny Cajuhi]

It seems that the Cray has PetSc, I am not sure about MUMPS and I would need it. ​

Well you don't need numdiff and you can load bzip2 from a module
right? My question is more do you just need to install p4est and deal
and you can load modules for everything else or do you need to install
your own Trilinos with all its dependencies or a specific version of
petsc. I have installed deal on a cray before and if you just need
p4est and deal, it shouldn't be too bad. Now if you need to install
your own superLU-dist for Trilinos, it's another beast...

I think numdiff and bzip2 are not available​. From the list of available modules in https://www.hlrn.de/home/view/System3/CraySoftware . Petsc, Mumps, SuperLu, Trilinos are available. P4est I need to install.

[Bruno Turcksin]

2017-06-01 11:17 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> I think numdiff and bzip2 are not available. From the list of available
> modules in https://www.hlrn.de/home/view/System3/CraySoftware . Petsc,
> Mumps, SuperLu, Trilinos are available. P4est I need to install.

But do you need all of these any way? Does your code uses both Petsc
and Trilinos? My point is if you don't use a package, deal doesn't
need it either. For example, why do you need numdiff? In deal, we use
it to run the testsuite which you don't want to do. So you probably
don't need to install numdiff.

[Tuanny Cajuhi]

You are right, thank you for the explanation. ​My code uses PetSc with MUMPS. Just the output is done by Trilinos (the idea of joint_fe). ​In summary, I need to add p4est.

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[Bruno Turcksin]

2017-06-01 11:37 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> You are right, thank you for the explanation. My code uses PetSc with MUMPS.
> Just the output is done by Trilinos (the idea of joint_fe). In summary, I
> need to add p4est.

Download p4est, untar it, and try something like this:

./configure CC=cc CXX=CC F77=ftn --enable-mpi --disable-vtk-binary
--without-blas --prefix=/wherever/you/want

I may still have some scripts to install deal on cray. I will look for
it tonight

[Tuanny Cajuhi]

Thanks a lot, Bruno. 

I will keep trying. 

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[Rene Gassmöller]

Hi Tuanny,

I happened to install deal.II on a Cray over the last days, and both compiled everything by hand and (afterwards) decided to write a candi script for it. Keep in mind that my instructions are for my specific setting and application, i.e. I compile deal.II with the packages p4est, trilinos, and petsc only, and do not know about other packages. The cluster is also a very specific system (Lonestar 5, of the Texas Advanced Computing Center), but yours is likely at least similar. Anyway, I hope this is of help to you.

The candi platform file with instructions on how to set up the environment is here:
https://github.com/gassmoeller/candi/blob/lonestar_config/deal.II-toolchain/platforms/lonestar5.platform

You can download it and use it with candi by adding the option --platform=FILENAME where FILENAME contains the full path to this file. On my cluster I had two problems with candi that I needed to change. You can find the modifications I did here: https://github.com/dealii/candi/pull/29 and https://github.com/dealii/candi/pull/30. They are not yet part of candi, so you will need to include them manually.

If you decide to compile manually instead let me know, I also have those commands somewhere (not as nicely formatted). The most important point are the loaded modules, environment variables, and compiler options all of which you can see inside the candi script.

Hope that helps a bit,
Rene

Am Donnerstag, 1. Juni 2017 09:53:01 UTC-6 schrieb Tuanny Cajuhi:

Thanks a lot, Bruno. 

I will keep trying. 

On Thu, Jun 1, 2017 at 5:50 PM, Bruno Turcksin <bruno.t...@gmail.com> wrote:

2017-06-01 11:37 GMT-04:00 Tuanny Cajuhi <trmc...@gmail.com>:
> You are right, thank you for the explanation. My code uses PetSc with MUMPS.
> Just the output is done by Trilinos (the idea of joint_fe). In summary, I
> need to add p4est.
Download p4est, untar it, and try something like this:

./configure CC=cc CXX=CC F77=ftn --enable-mpi --disable-vtk-binary
--without-blas --prefix=/wherever/you/want

I may still have some scripts to install deal on cray. I will look for
it tonight

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[Rene Gassmöller]

I updated the github branch. The file is not longer at the old position, instead take a look at: https://github.com/dealii/candi/pull/31

Best
Rene

[Tuanny Cajuhi]

Hi Rene,

thank you so much for sharing and for the explanation!!! I will try and keep you updated :)

Best,
Tuanny

[Tuanny Cajuhi]

Hi Rene,

your explanation helped me a lot!! :)) I was able to run up to this point:

[100%] Building CXX object source/numerics/CMakeFiles/obj_numerics_release.dir/vector_tools_rhs.cc.o
Linking CXX shared library ../lib/libdeal_II.g.so
/usr/bin/ld.gold: error: cannot find -lAtpSigHandler
/usr/bin/ld.gold: error: cannot find -lAtpSigHCommData
collect2: error: ld returned 1 exit status
make[2]: *** [lib/libdeal_II.g.so.8.5.0] Error 1
make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Built target obj_numerics_release
make: *** [all] Error 2
Failure with exit status: 2
Exit message: There was a problem building dealii v8.5.0.

Have you ever had this error? One colleague of mine got the same error when installing everything manually. Could it be something related to the cray, e.g. additional module?

Thank you!

Best,
Tuanny

On 03.06.2017 20:14, Rene Gassmöller wrote:

[Rene Gassmoeller]

Hi Tuanny,

That is good to hear. Unfortunately I have not seen the error message before. AtpSigHandler seems to be some cray specific library, and it is a bit surprising that your linker does not seem to find it. Maybe you can try finding out in which module it is packaged or ask your cluster support for help. To me this does not look like a deal.II specific problem.

Another idea would be to check if /usr/bin/ld.gold is the linker you should use, or if the build system picks up he wrong linker.

Best

 Rene

[Tuanny Cajuhi]

Hi Rene,

I asked them and as soon as I get an update I will post it here. My colleague also mentioned that it could be something related to the linker.
In any case, I am really happy that the installation got this far and I am hoping to use deal.II asap in the cluster. Thank you again, will keep you posted :))

Best,
Tuanny

[Tuanny Cajuhi]

Hi Rene,

is it possible to include MUMPS to the platform file? 

An error occurred in line <846> of file </home/h/niitcaju/deal.ii-candi/tmp/unpack/deal.II-v8.5.0/source/lac/petsc_solver

.cc> in function

   void dealii::PETScWrappers::SparseDirectMUMPS::solve(const dealii::PETScWrappers::MatrixBase&, dealii::PETScWrappers:

:VectorBase&, const dealii::PETScWrappers::VectorBase&)

The violated condition was:  

   false

Additional information:  

   Your PETSc installation does not include a copy of the MUMPS package necessary for this solver. You will need to conf

igure PETSc so that it includes MUMPS, recompile it, and then re-configure and recompile deal.II as well.

Thank you,

Tuanny 

PS: Unloading the module atp helped to solve the problem I mentioned in the previous message. 

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[Rene Gassmöller]

Hi Tuanny,

I am not quite sure what is happening there (I do not have much experience with PETSc or MUMPS). As far as I can see MUMPS is not a separate package for deal.II but needs to be installed with PETSc. Maybe somebody else knows which options need to be added to the petsc.package file of candi to make MUMPS work? Or if you can find the options for me, I can modify the file accordingly. Is it possible that this has to do with the fact I removed the other default packages, except for p4est, trilinos and petsc?

Best,

Rene

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[Timo Heister]

> I am not quite sure what is happening there (I do not have much experience
> with PETSc or MUMPS). As far as I can see MUMPS is not a separate package
> for deal.II but needs to be installed with PETSc.

corect.

> Maybe somebody else knows
> which options need to be added to the petsc.package file of candi to make
> MUMPS work?

If you look at petsc.package you can see that you need to have
parmetis enabled to get mumps support, which is enabled by default.

[Rene Gassmöller]

@Timo: Thanks for the confimation and feedback.
I needed to do some adjustments to candi to get parmetis to run, but a combination of https://github.com/dealii/candi/pull/33 and https://github.com/dealii/candi/pull/32 should now be able to automatically install deal.II on most Cray machines. @Tuanny: Could you give that a try?

Best,
Rene