Can you try Lawrence's suggestion of trying to compile a simple Fortran code using mpif90: $ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello (The $s indicate a shell prompt). all the best --cjc On 30 November 2015 at 16:05, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
Tried:
1) Updating .profile as suggested by Justin
2) Reinstalled home-brew after uninstalling it.
3) But the hello.world fortran code still crashes.
4) Hence, same error message holds.
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work.
Cannot compile FC with /usr/local/bin/mpif90.
*******************************************************************************
...
----------------------------------------
Command "//anaconda/bin/python -c "import setuptools, tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-YcsuFy-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-build
Any suggestions?
------------------------------ *From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Justin Chang <jychang48@gmail.com> *Sent:* Monday, November 30, 2015 3:53 PM *To:* Firedrake Project
*Subject:* Re: [firedrake] FD on mac
Miklos,
Yes my error has been resolved by recompiling spatialindex with the same homebrew compilers as was used for firedrake
Thanks Justin
On Mon, Nov 30, 2015 at 3:29 AM, Miklós Homolya < m.homolya14@imperial.ac.uk> wrote:
Please let me know if that fixes your problem.
On 28/11/15 20:08, Justin Chang wrote:
Ah right, didn't think about that. Got it, thanks!
On Sat, Nov 28, 2015 at 3:35 AM, Miklós Homolya < m.homolya14@imperial.ac.uk> wrote:
With respect to the libspatialindex problem:
Yes, see https://github.com/firedrakeproject/firedrake/issues/640
I suggest you to try rebuilding libspatialindex from source (you can do that with homebrew) using the same compiler as you used to build firedrake.
On 28/11/15 07:11, Justin Chang wrote:
Hi all,
I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile:
export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5
and rebuilt openmpi via:
brew reinstall openmpi --build-from-source
Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module:
python -c 'from firedrake import *'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module>
from firedrake.assemble import *
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module>
from firedrake import assemble_expressions
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module>
from firedrake import function
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module>
from firedrake import functionspace
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module>
import firedrake.mesh as mesh_t
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module>
import firedrake.spatialindex as spatialindex
ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE
Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Expected in: flat namespace
in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Looks like something went awry with spatialindex. Anyone else having this problem?
Thanks, Justin
On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell < <lawrence.mitchell@imperial.ac.uk>lawrence.mitchell@imperial.ac.uk> wrote:
On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS?
Hopefully not!
From: firedrake-bounces@imperial.ac.uk < firedrake-bounces@imperial.ac.uk> on behalf of Wingate, Beth < <B.Wingate@exeter.ac.uk>B.Wingate@exeter.ac.uk> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working:
TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see
configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with
--with-fc=/usr/local/bin/mpif90 does not work.
Cannot compile FC with /usr/local/bin/mpif90.
*******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens?
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
Cheers,
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916
Oh, you did this, sorry. On 30 November 2015 at 16:09, Colin Cotter <colin.cotter@imperial.ac.uk> wrote:
Can you try Lawrence's suggestion of trying to compile a simple Fortran code using mpif90:
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
(The $s indicate a shell prompt).
all the best --cjc
On 30 November 2015 at 16:05, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
Tried:
1) Updating .profile as suggested by Justin
2) Reinstalled home-brew after uninstalling it.
3) But the hello.world fortran code still crashes.
4) Hence, same error message holds.
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work.
Cannot compile FC with /usr/local/bin/mpif90.
*******************************************************************************
...
----------------------------------------
Command "//anaconda/bin/python -c "import setuptools, tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-YcsuFy-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-build
Any suggestions?
------------------------------ *From:* firedrake-bounces@imperial.ac.uk < firedrake-bounces@imperial.ac.uk> on behalf of Justin Chang < jychang48@gmail.com> *Sent:* Monday, November 30, 2015 3:53 PM *To:* Firedrake Project
*Subject:* Re: [firedrake] FD on mac
Miklos,
Yes my error has been resolved by recompiling spatialindex with the same homebrew compilers as was used for firedrake
Thanks Justin
On Mon, Nov 30, 2015 at 3:29 AM, Miklós Homolya < m.homolya14@imperial.ac.uk> wrote:
Please let me know if that fixes your problem.
On 28/11/15 20:08, Justin Chang wrote:
Ah right, didn't think about that. Got it, thanks!
On Sat, Nov 28, 2015 at 3:35 AM, Miklós Homolya < m.homolya14@imperial.ac.uk> wrote:
With respect to the libspatialindex problem:
Yes, see https://github.com/firedrakeproject/firedrake/issues/640
I suggest you to try rebuilding libspatialindex from source (you can do that with homebrew) using the same compiler as you used to build firedrake.
On 28/11/15 07:11, Justin Chang wrote:
Hi all,
I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile:
export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5
and rebuilt openmpi via:
brew reinstall openmpi --build-from-source
Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module:
python -c 'from firedrake import *'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module>
from firedrake.assemble import *
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module>
from firedrake import assemble_expressions
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module>
from firedrake import function
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module>
from firedrake import functionspace
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module>
import firedrake.mesh as mesh_t
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module>
import firedrake.spatialindex as spatialindex
ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE
Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Expected in: flat namespace
in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Looks like something went awry with spatialindex. Anyone else having this problem?
Thanks, Justin
On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell < <lawrence.mitchell@imperial.ac.uk>lawrence.mitchell@imperial.ac.uk> wrote:
On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS?
Hopefully not!
From: firedrake-bounces@imperial.ac.uk < firedrake-bounces@imperial.ac.uk> on behalf of Wingate, Beth < <B.Wingate@exeter.ac.uk>B.Wingate@exeter.ac.uk> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working:
TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see
configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with
--with-fc=/usr/local/bin/mpif90 does not work.
Cannot compile FC with /usr/local/bin/mpif90.
*******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens?
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
Cheers,
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-- http://www.imperial.ac.uk/people/colin.cotter
www.cambridge.org/9781107663916
-- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916
On Onno's macbook: cat > hello.f90 << EOF
program main use mpi implicit none write(*, *)'Hello world' end program EOF math-mc1097:werk amtob$ mpif90 hello.f90 -o hello
No underlying compiler was specified in the wrapper compiler data file (e.g., mpicc-wrapper-data.txt) -------------------------------------------------------------------------- math-mc1097:werk amtob$ On Floriane's: With mpi I don't have an error at 'EOF', but the next command ('$ mpif90 hello.f90 -o hello') does not work. Error: " -bash: $: command not found" ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: Monday, November 30, 2015 4:11 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac On 30/11/15 16:09, Colin Cotter wrote:
use mph
use mpi
On 30 Nov 2015, at 17:04, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
------------------------------------- No underlying compiler was specified in the wrapper compiler data file (e.g., mpicc-wrapper-data
Ok, so there is no fortran compiler available. I thought our install script installed one, but plausibly that failed to work. Lawrence
with me but florin has it working now she forgot to remove the prompt I think I have the same os as Floriane, installed anaconda, reinstalled home-brew but that did not work. ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: Monday, November 30, 2015 5:25 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
On 30 Nov 2015, at 17:04, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
------------------------------------- No underlying compiler was specified in the wrapper compiler data file (e.g., mpicc-wrapper-data
Ok, so there is no fortran compiler available. I thought our install script installed one, but plausibly that failed to work. Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
I don't think Onno is using the installation script but the old step-by-step instructions. I am right, Onno? The installation script does not work on my Mac either; I reported it some time ago but did not get any update from you. It seems that it might not work on Mavericks OS (?) Best, Anna. On 30/11/15 17:27, Onno Bokhove wrote:
with me but florin has it working now she forgot to remove the prompt I think I have the same os as Floriane, installed anaconda, reinstalled home-brew but that did not work.
________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: Monday, November 30, 2015 5:25 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
On 30 Nov 2015, at 17:04, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
------------------------------------- No underlying compiler was specified in the wrapper compiler data file (e.g., mpicc-wrapper-data Ok, so there is no fortran compiler available. I thought our install script installed one, but plausibly that failed to work.
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-- Dr Anna Kalogirou Research Fellow School of Mathematics University of Leeds http://www1.maths.leeds.ac.uk/~matak/
Yes, the script does not work either. ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Anna Kalogirou <a.kalogirou@leeds.ac.uk> Sent: Monday, November 30, 2015 5:34 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac I don't think Onno is using the installation script but the old step-by-step instructions. I am right, Onno? The installation script does not work on my Mac either; I reported it some time ago but did not get any update from you. It seems that it might not work on Mavericks OS (?) Best, Anna. On 30/11/15 17:27, Onno Bokhove wrote:
with me but florin has it working now she forgot to remove the prompt I think I have the same os as Floriane, installed anaconda, reinstalled home-brew but that did not work.
________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: Monday, November 30, 2015 5:25 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
On 30 Nov 2015, at 17:04, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
------------------------------------- No underlying compiler was specified in the wrapper compiler data file (e.g., mpicc-wrapper-data Ok, so there is no fortran compiler available. I thought our install script installed one, but plausibly that failed to work.
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-- Dr Anna Kalogirou Research Fellow School of Mathematics University of Leeds http://www1.maths.leeds.ac.uk/~matak/ _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (4)
-
Anna Kalogirou
-
Colin Cotter
-
Lawrence Mitchell
-
Onno Bokhove