[deal.II] 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

Post by Roc Wang
* 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

Post by 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
*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]

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

Post by 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
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

Post by 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
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
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!!

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['Uwe Köcher' via deal.II User Group]

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

Post by 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
*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

Post by 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
*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!!*

[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,

Post by Tuanny Cajuhi
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.

Post by Tuanny Cajuhi
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

Post by Bruno Turcksin
Tuanny,

Post by Tuanny Cajuhi
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)

‘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.

Post by Tuanny Cajuhi
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
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*[phone]*

[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

Post by 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/
configure: error: Fortran 77 compiler cannot create executables
See `config.log' for more details
Best regards,
Tuanny

Post by Bruno Turcksin
Tuanny,

Post by Tuanny Cajuhi
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)

‘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.

Post by Tuanny Cajuhi
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
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rum/dealii?hl=en
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*[phone] <0176%2032319185>*

--
*Tuanny Cajuhi*
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*[phone]*

[Bruno Turcksin]

Tuanny,

Post by Tuanny Cajuhi
My next issue is p4est...

:-(

Post by Tuanny Cajuhi
Build FAST version 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

Post by Bruno Turcksin
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

Post by Tuanny Cajuhi
Hi Bruno,
thank you.

Post by Bruno Turcksin
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!
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[Tuanny Cajuhi]

I did not find any of them... :/

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

Post by Tuanny Cajuhi
Hi Bruno,
thank you.

Post by Bruno Turcksin
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!
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[Bruno Turcksin]

Post by Tuanny Cajuhi
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

Post by Bruno Turcksin

Post by Tuanny Cajuhi
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?
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[Bruno Turcksin]

Post by 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

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]

Post by Bruno Turcksin
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

Post by Bruno Turcksin
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?

Post by Bruno Turcksin
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]

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. ​

Post by Bruno Turcksin
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]

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.

Post by Bruno Turcksin

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.
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*[phone]*

[Bruno Turcksin]

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.

Post by 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.

./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
--
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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*Tuanny Cajuhi*
*Computational Sciences in Engineering, **MSc *

*[phone]*

[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

Post by Tuanny Cajuhi
Thanks a lot, Bruno.
I will keep trying.

Post by 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.

./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
--
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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--
*Tuanny Cajuhi*
*Computational Sciences in Engineering, **MSc *
*[phone]*

[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

Post by 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
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

Post by Tuanny Cajuhi
Thanks a lot, Bruno.
I will keep trying.

Post by 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.

./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
--
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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--
*Tuanny Cajuhi*
*Computational Sciences in Engineering, **MSc *
*[phone]*

[Tuanny Cajuhi]

Hi Rene,

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

Best,
Tuanny

Post by 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
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
https://github.com/gassmoeller/candi/blob/lonestar_config/deal.II-toolchain/platforms/lonestar5.platform
<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
https://github.com/dealii/candi/pull/29
<https://github.com/dealii/candi/pull/29> and
https://github.com/dealii/candi/pull/30
<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
Thanks a lot, Bruno.
I will keep trying.
On Thu, Jun 1, 2017 at 5:50 PM, Bruno Turcksin

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.

./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
--
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
<https://groups.google.com/d/forum/dealii?hl=en>
---
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For more options, visit https://groups.google.com/d/optout
<https://groups.google.com/d/optout>.
--
/Tuanny Cajuhi/
/Computational Sciences in Engineering, //MSc /
/[phone]
/
--
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[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

Post by 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
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
https://github.com/gassmoeller/candi/blob/lonestar_config/deal.II-toolchain/platforms/lonestar5.platform
<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
https://github.com/dealii/candi/pull/29
<https://github.com/dealii/candi/pull/29> and
https://github.com/dealii/candi/pull/30
<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

[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-------- Original message --------From: Tuanny Cajuhi <***@gmail.com> Date: 6/3/2017 21:13 (GMT-05:00) To: ***@googlegroups.com Subject: Re: [deal.II] Re: get errors when installing dealii on openSUSE Leap 42.1 by using candi

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:



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



Am Freitag, 2. Juni 2017 14:55:45 UTC-4 schrieb 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

[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

Post by Rene Gassmöller
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
-------- Original message --------
Date: 6/3/2017 21:13 (GMT-05:00)
Subject: Re: [deal.II] Re: get errors when installing dealii on
openSUSE Leap 42.1 by using candi
Hi Rene,
[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

Post by 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
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
https://github.com/gassmoeller/candi/blob/lonestar_config/deal.II-toolchain/platforms/lonestar5.platform
<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
https://github.com/dealii/candi/pull/29
<https://github.com/dealii/candi/pull/29> and
https://github.com/dealii/candi/pull/30
<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

--
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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[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.

Post by 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
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
-------- Original message --------
Date: 6/3/2017 21:13 (GMT-05:00)
Subject: Re: [deal.II] Re: get errors when installing dealii on openSUSE
Leap 42.1 by using candi
Hi Rene,
[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
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

Post by 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
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
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

--
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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[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

Post by 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
:VectorBase&, const dealii::PETScWrappers::VectorBase&)
false
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.

Post by 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
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
-------- Original message --------
Date: 6/3/2017 21:13 (GMT-05:00)
Subject: Re: [deal.II] Re: get errors when installing dealii on openSUSE
Leap 42.1 by using candi
Hi Rene,
[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
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

Post by 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
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
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

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[Timo Heister]

Post by Rene Gassmöller
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.

Post by Rene Gassmöller
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

Post by Rene Gassmöller

Post by Rene Gassmöller
I am not quite sure what is happening there (I do not have much

experience

Post by Rene Gassmöller
with PETSc or MUMPS). As far as I can see MUMPS is not a separate

package

Post by Rene Gassmöller
for deal.II but needs to be installed with PETSc.

corect.

Post by Rene Gassmöller
Maybe somebody else knows
which options need to be added to the petsc.package file of candi to

make

Post by Rene Gassmöller
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.