"Make test" failure following Trilinos installation with Mesquite

[Oded Yaakobi]

Dear all,

 

Following Wolfgang’s suggestion to use Mesquite for improving the mesh quality in my problem (see

https://groups.google.com/forum/#!searchin/dealii/Mesquite%7Csort:relevance/dealii/f3jWQ7DPeYA/aCCgEUSVAQAJ),

I installed Trilinos on my laptop (Mac OS X Yosemite Version 10.10.5).

 

I had various problems with the installation of the most recent versions of Trilinos - I were not able to install Trilinos 12.6.2 or 12.6.3 with all the required packages for deal.ii, and for some reason Trilinos 12.6.1 does not include Mesquite. I ended up with installing Trilinos 12.4.2 and installing dealii 8.4.1 with it. Everything in the installation seemed to be fine, but when I run “make test”, all the tests failed. You may see the attached log file.

 

Does anybody have any idea how to fix this problem?

 

Thanks,

Oded

 

 

[Bruno Turcksin]

Oded,

libmsqutil.12, i.e mesquite, is not loaded. In linux, you would need to add it to your LD_LIBRARY_PATH but I don't know how it works on Mac.

Best,

Bruno

[Denis Davydov]

Hi Oded,

AFAIK DYLD_LIBRARY_PATH won't work on El Capitan unless you turn off System Integrity Protection. So you have several options:

(i) use binary package for mac https://www.dealii.org/download.html

(ii) compile dealiii using Spack, which uses RPATHs in linking https://github.com/LLNL/spack and thereby supports coexistence of different variants/versions of software. There is no need to manipulate LD_LIBRARY_PATH there.

(iii) use Homebrew which installs everything in /usr/local/lib and /usr/local/include and so libraries are picked up automatically.

p.s. I used to use (iii) but now switched to (ii).

Regards,

Denis.

[Oded Yaakobi]

Hi Denis,

 

Thank you very much for your suggestions. Unfortunately, none of your suggestions worked for me.

 

(i) I installed dealii binary package but it does not include Mesquite.

Is it possible to include Mesquite into dealii binary package?

 

 

(ii) I downloaded the most recent version of Spack (version 0.8.17), but its installation failed. You may see below the error message that I got:

 

==> Installing libelf

==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz

######################################################################## 100.0%

==> Staging archive: /Users/yaakobioy/spack/spack-0.8.17/var/spack/stage/lib...@0.8.13%g...@5.2.0=macosx_10.10_x86_64/libelf-0.8.13.tar.gz

==> Created stage in /Users/yaakobioy/spack/spack-0.8.17/var/spack/stage/lib...@0.8.13%g...@5.2.0=macosx_10.10_x86_64.

==> No patches needed for libelf.

==> Building libelf.

creating cache ./config.cache

checking whether make sets ${MAKE}... yes

checking for gcc... cc

checking whether the C compiler (cc  ) works... no

configure: error: installation or configuration problem: C compiler cannot create executables.

==> Error: command './configure --prefix=/Users/yaakobioy/spack/spack-0.8.17/opt/macosx_10.10_x86_64/g...@5.2.0/lib...@0.8.13 --enable-shared --disable-dependency-tracking --disable-debug' returned error code 1

 

 

Do you know how to fix this problem?

 

I also tried to install previous versions of Spack (0.8.11, 0.8.15 and 0.8.16) and failed with each one of them, although with different error messages in each case.

 

 

(iii) I installed Homebrew, but it is not clear to me what should I do next. If the other two aforementioned routes are not possible, could you please advise me how to should use Homebrow?

 

Best,

Oded

            

[Bruno Turcksin]

Oded,

2016-05-20 13:25 GMT-04:00 Oded Yaakobi <oded.y...@nih.gov>:
> (ii) I downloaded the most recent version of Spack (version 0.8.17), but its
> installation failed. You may see below the error message that I got:

You need to use the development version on github.

Best,

Bruno

[Oded Yaakobi]

Hi Bruno,

I forgot to mention that I also tried the development version of Spack and it didn't work. Here is the error message that I got:

==> Installing libelf

==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz

######################################################################## 100.0%

==> Staging archive: /Users/yaakobioy/spack/spack-develop_20-05-2016/var/spack/stage/libelf-0.8.13-zxsi3c75tqcmgck7r562bgi75svg7h3s/libelf-0.8.13.tar.gz

==> Created stage in /Users/yaakobioy/spack/spack-develop_20-05-2016/var/spack/stage/libelf-0.8.13-zxsi3c75tqcmgck7r562bgi75svg7h3s

==> No patches needed for libelf

==> Building libelf

==> Error: Command exited with status 1:

'./configure' '--prefix=/Users/yaakobioy/spack/spack-develop_20-05-2016/opt/spack/darwin-x86_64/gcc-5.2.0/libelf-0.8.13-zxsi3c75tqcmgck7r562bgi75svg7h3s' '--enable-shared' '--disable-dependency-tracking' '--disable-debug'

See build log for details:

  /private/var/folders/pr/4tmsr5x51vs5f2bt2gqscp9hv0l_l7/T/yaakobioy/spack-stage/spack-stage-YhBV13/libelf-0.8.13/spack-build.out

/Users/yaakobioy/spack/spack-develop_20-05-2016/var/spack/repos/builtin/packages/libelf/package.py:45, in install:

     41       def install(self, spec, prefix):

     42           configure("--prefix=" + prefix,

     43                     "--enable-shared",

     44                     "--disable-dependency-tracking",

  >> 45                     "--disable-debug")

     46           make()

     47   

     48           # The mkdir commands in libelf's install can fail in parallel

     49           make("install", parallel=False)

==> Error: Installation process had nonzero exit code.

Best,

Oded

[Bruno Turcksin]

Oded,

can you post this file:

2016-05-20 14:05 GMT-04:00 Oded Yaakobi <oded.y...@nih.gov>:
> /private/var/folders/pr/4tmsr5x51vs5f2bt2gqscp9hv0l_l7/T/yaakobioy/spack-stage/spack-stage-YhBV13/libelf-0.8.13/spack-build.out

Best,

Bruno

[Oded Yaakobi]

Sure,

Attached is the file.

Oded

[Bruno Turcksin]

Oded,

there is a problem with your compiler :-( It says that gcc doesn't
work for some reason. Here is the documentation on spack concerning
the compiler http://software.llnl.gov/spack/basic_usage.html#compiler-configuration
Unfortunately, I don't have a mac so I can't help you but Denis should
know what to do.

Best,

Bruno

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[Denis Davydov]

Hi Oded,

On Friday, May 20, 2016 at 7:25:42 PM UTC+2, Oded Yaakobi wrote:

 

(i) I installed dealii binary package but it does not include Mesquite.

Is it possible to include Mesquite into dealii binary package?

I think Luca could comment on that.

  

(ii) I downloaded the most recent version of Spack (version 0.8.17), but its installation failed.

Try master branch which is 0.9.1: https://github.com/LLNL/spack/tree/master

 

You may see below the error message that I got:

 

==> Installing libelf

==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz

######################################################################## 100.0%

==> Staging archive: /Users/yaakobioy/spack/spack-0.8.17/var/spack/stage/libelf@0.8.13%g...@5.2.0=macosx_10.10_x86_64/libelf-0.8.13.tar.gz

==> Created stage in /Users/yaakobioy/spack/spack-0.8.17/var/spack/stage/libelf@0.8.13%g...@5.2.0=macosx_10.10_x86_64.

==> No patches needed for libelf.

==> Building libelf.

creating cache ./config.cache

checking whether make sets ${MAKE}... yes

checking for gcc... cc

checking whether the C compiler (cc  ) works... no

You certainly have some issues with your C compiler (clang) on OSX.

Do you have XCode installed? If not, do so.

You also need to have command-line tools, run: xcode-select --install

After installing this, delete the following configure file: ~/.spack/compilers.yaml

The step-by-step instruction is as follows:

(0) add the following to bash

```

SPACK_ROOT=/path/to/spack

export PATH=$SPACK_ROOT/bin:$PATH

``` 

make sure c/c++/fortran compilers are in path. You will need gfortran from GCC:

(1) 

```

spack install g...@5.3.0

spack install environment-modules

```

(2) setup environment modules in bash (fill `<xyz>` accordingly by checking the folder structure)

```

source $SPACK_ROOT/opt/spack/<platform>/<compiler>/environment-modules-<ver>-<hash>/Modules/init/bash

. $SPACK_ROOT/share/spack/setup-env.sh

```

(3) load installed gcc and let spack update compilers list:

```

spack load gcc

spack compiler find

```

(4) install deal.ii with everything possible turned on

```

spack install dealii%gcc

```

(5) use 

```

spack load dealii

spack load cmake

$echo $DEAL_II_DIR

$which cmake

```

configure: error: installation or configuration problem: C compiler cannot create executables.

==> Error: command './configure --prefix=/Users/yaakobioy/spack/spack-0.8.17/opt/macosx_10.10_x86_64/g...@5.2.0/libelf@0.8.13 --enable-shared --disable-dependency-tracking --disable-debug' returned error code 1

 

 

Do you know how to fix this problem?

Regards,

Denis. 

[Denis Davydov]

p.s. one can also make Clang + gfortran work, but this is de-factor mixing of compilers and requires hacking two-three lines to work properly. For starters you can try pure GCC build.

[Oded Yaakobi]

Hi Denis,

 

Thank you for your detailed response.

 

It tried the master branch of spack but it didn’t work either, giving similar error messages (see also the attached file):

 

==> Installing libelf

==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz

######################################################################## 100.0%

==> Staging archive: /Users/yaakobioy/spack/spack-master_20-05-2016/var/spack/stage/libelf-0.8.13-2lwz26yxoxecb2lwuwhaj7wwlvziuozz/libelf-0.8.13.tar.gz

==> Created stage in /Users/yaakobioy/spack/spack-master_20-05-2016/var/spack/stage/libelf-0.8.13-2lwz26yxoxecb2lwuwhaj7wwlvziuozz

==> No patches needed for libelf

==> Building libelf

==> Error: Command exited with status 1:

'./configure' '--prefix=/Users/yaakobioy/spack/spack-master_20-05-2016/opt/spack/darwin-x86_64/gcc-5.2.0/libelf-0.8.13-2lwz26yxoxecb2lwuwhaj7wwlvziuozz' '--enable-shared' '--disable-dependency-tracking' '--disable-debug'

 

See build log for details:

  /private/var/folders/pr/4tmsr5x51vs5f2bt2gqscp9hv0l_l7/T/yaakobioy/spack-stage/spack-stage-vi8kK8/libelf-0.8.13/spack-build.out

 

/Users/yaakobioy/spack/spack-master_20-05-2016/var/spack/repos/builtin/packages/libelf/package.py:45, in install:

     41       def install(self, spec, prefix):

     42           configure("--prefix=" + prefix,

     43                     "--enable-shared",

     44                     "--disable-dependency-tracking",

  >> 45                     "--disable-debug")

     46           make()

     47  

     48           # The mkdir commands in libelf's install can fail in parallel

     49           make("install", parallel=False)

==> Error: Installation process had nonzero exit code.

 

 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 

I followed your instructions about Xcode (which I already installed before), but encountered a problem also in this direction. You may see the history of my commands:

 

[ yaakobioy L02029080  ~/spack/spack-master_20-05-2016/bin ]$ xcode-select --install

xcode-select: error: command line tools are already installed, use "Software Update" to install updates

[ yaakobioy L02029080  ~/spack/spack-master_20-05-2016/bin ]$ cd ~/.spack/

[ yaakobioy L02029080  ~/.spack ]$ ls

compilers.yaml

[ yaakobioy L02029080  ~/.spack ]$ rm compilers.yaml

remove compilers.yaml? y

[ yaakobioy L02029080  ~/.spack ]$ ls

[ yaakobioy L02029080  ~/.spack ]$ SPACK_ROOT=/path/to/spack

[ yaakobioy L02029080  ~/.spack ]$ export PATH=$SPACK_ROOT/bin:$PATH

[ yaakobioy L02029080  ~/.spack ]$ spack install g...@5.3.0

-bash: spack: command not found

 

Best,

Oded

 

 

 

[Denis Davydov]

Hi Oded,

Here are instructions again with a bit more explanation as I noticed that you don't follows them exactly:

(0) add the following to ~/.bash_profile  (DO NOT RUN IN TERMINAL)

```

SPACK_ROOT=/path/to/spack

export PATH=$SPACK_ROOT/bin:$PATH

``` 

Run new terminal window and install GCC and environment-modules package:

(1) 

```

spack install g...@5.3.0

spack install environment-modules

```

(2) add the following to ~/.bash_profile (fill `<xyz>` accordingly by checking the folder structure)

```

source $SPACK_ROOT/opt/spack/<platform>/<compiler>/environment-modules-<ver>-<hash>/Modules/init/bash

. $SPACK_ROOT/share/spack/setup-env.sh

```

(3) Run new terminal windows and load installed gcc and let spack update compilers list:

```

spack load gcc

spack compiler find

```

(4) install deal.ii with everything possible turned on

```

spack install dealii%gcc

```

(5) use 

```

spack load dealii

spack load cmake

$echo $DEAL_II_DIR

$which cmake

```

Regards,

Denis.

[Oded Yaakobi]

Hi Denis,

 

I tried to follow your instructions but got an error message.

 

(0)  (0) add the following to ~/.bash_profile  (DO NOT RUN IN TERMINAL)

 

I didn’t find the file “.bash_profile” at “~/” directory. You may see the files that are there:

[ yaakobioy L02029080  ~ ]$ ls -a

.           .anyconnect     .profile        Desktop           Movies               dealii

..          .bash_history       .rstudio-desktop   Development          Music                spack

.CFUserTextEncoding .bashrc         .spack         Documents      Pictures       workspace

.DS_Store       .config         .spackconfig       Downloads      Public

.RData          .cups           .ssh            Doxygen            TriBITS

.Rhistory       .eclipse        .subversion     GCC           Trilinos

.Trash          .lldb           Applications       Library              boost_1_56_0

.account        .p2         CPPUnit         Mesquite          config_aux

 

I guess that you referred to the file “.profile”.

 

################################################################

 

```

SPACK_ROOT=/path/to/spack

export PATH=$SPACK_ROOT/bin:$PATH

``` 

 

I added these two lines to the file “.profile”. The content of the modified file is:

 

export PATH=/Applications/CMake.app/Contents/bin:$PATH

export DEAL_II_CONF_SILENT=ON

   . /Applications/deal.II.app/Contents/Resources/share/deal.II/dealii.conf

export PATH=/Applications/CMake.app/Contents/bin:$PATH

SPACK_ROOT=/Users/yaakobioy/spack/spack-master_20-05-2016/

export PATH=$SPACK_ROOT/bin:$PATH

 

 

################################################################

 

 

Run new terminal window and install GCC and environment-modules package:

(1) 

```

spack install g...@5.3.0

 

I run this command and got the following error message:

 

[ yaakobioy L02029080  ~/spack/spack-master_20-05-2016/bin ]$ spack install g...@5.3.0

==> Installing gcc

==> Installing gmp

==> Installing m4

==> Installing libsigsegv

==> Already downloaded /Users/yaakobioy/spack/spack-master_20-05-2016/var/spack/stage/libsigsegv-2.10-h43d2fuzsdysa2ctr3qsxpk55etk4dzv/libsigsegv-2.10.tar.gz

==> Already staged libsigsegv-2.10-h43d2fuzsdysa2ctr3qsxpk55etk4dzv in /Users/yaakobioy/spack/spack-master_20-05-2016/var/spack/stage/libsigsegv-2.10-h43d2fuzsdysa2ctr3qsxpk55etk4dzv

==> No patches needed for libsigsegv

==> Building libsigsegv

==> Error: Command exited with status 77:

'./configure' '--prefix=/Users/yaakobioy/spack/spack-master_20-05-2016/opt/spack/darwin-x86_64/gcc-5.2.0/libsigsegv-2.10-h43d2fuzsdysa2ctr3qsxpk55etk4dzv' '--enable-shared'

 

See build log for details:

  /private/var/folders/pr/4tmsr5x51vs5f2bt2gqscp9hv0l_l7/T/yaakobioy/spack-stage/spack-stage-acoxgL/libsigsegv-2.10/spack-build.out

 

/Users/yaakobioy/spack/spack-master_20-05-2016/var/spack/repos/builtin/packages/libsigsegv/package.py:36, in install:

     34       def install(self, spec, prefix):

     35           configure('--prefix=%s' % prefix,

  >> 36                     '--enable-shared')

     37  

     38           make()

     39           make("install")

==> Error: Installation process had nonzero exit code.

 

################################################################

 

The content of the resulting spack-build.out file is:

 

==> './configure' '--prefix=/Users/yaakobioy/spack/spack-master_20-05-2016/opt/spack/darwin-x86_64/gcc-5.2.0/libsigsegv-2.10-h43d2fuzsdysa2ctr3qsxpk55etk4dzv' '--enable-shared'  Build Tools: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... build-aux/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for gcc... /Users/yaakobioy/spack/spack-master_20-05-2016/lib/spack/env/gcc/gcc checking whether the C compiler works... no configure: error: in `/private/var/folders/pr/4tmsr5x51vs5f2bt2gqscp9hv0l_l7/T/yaakobioy/spack-stage/spack-stage-acoxgL/libsigsegv-2.10': configure: error: C compiler cannot create executables See `config.log' for more details

 

 

################################################################

 

Do you have any suggestions what do to next?

 

Best,

Oded

[Denis Davydov]

Hi Oded,

It all goes back to the same error: 

 configure: error: C compiler cannot create executables See `config.log' for more details

It is hard to say what is actually wrong at  your system. Just try to make sure that you have as clean environment as possible

(no homebrew, no macports, just pure OSX + XCode + command line tools). My best guess is that you have somewhat polluted environment.

You can check that ~/.spack/compilers.yaml to see which compilers are being used, check if those are provided by OSX and not

some left-overs from somewhere else which happen to be broken. For me most recent XCode you should have:

compilers:

  darwin-x86_64:

    cl...@7.3.0-apple:

      cc: /usr/bin/clang

      cxx: /usr/bin/clang++

      f77: null

      fc: null

    g...@4.2.1:

      cc: /usr/bin/gcc

      cxx: /usr/bin/g++

      f77: null

      fc: null

Regards,

Denis.

[luca.heltai]

Sorry for replying late…

You could try this package:

https://github.com/luca-heltai/dealii/releases/tag/v8.5.0pre.v2

It is a deal.II library on steroids (650MB), with a full brew installation inside. I installed the brew tree under

/Applications/deal.II.brew.app/Contents/Resources/brew/

which means you can install any other package you may require by adding

/Applications/deal.II.brew.app/Contents/Resources/brew/bin

to the path (which is what the deal.II.brew.app does).

This is equivalent to following the instruction on the wiki on installing deal.II using brew, but it has been done for you.

Let me know if this works (messquite is installed in this version).

Best,

Luca.

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[Oded Yaakobi]

Hi Luca,

 

I appreciate very much the help of you, Denis and Bruno!

 

I spent some time today trying to follow your guidelines, but still weren’t able to figure everything out. I need some more time to work on that, since I am not sure that I completely understand all the steps that I should take. I will let you know in the next days what is the status of things.

 

Best,

Oded  

[Denis Davydov]

FYI, I created a FAQ page for using deal.II with Spack: https://github.com/dealii/dealii/wiki/deal.II-in-Spack

However given your compiler issue, i think in this case it will be easier to use Luca's prebuilt deal.II suite.

Regards,

Denis.

[Oded Yaakobi]

Hi Luca,

 

I am happy to let you know that I was able to install successfully the brew-based package using its source code. My application seems to run properly with this Mesquite-supported deal-ii installation.

 

Thank you very much for your help!

Oded