Re: [firedrake] Installation on macOS Sierra
Dear Hiroe, This is a known issue on Mac. The parallel test harness is not compatible with OpenMPI 3.0.0. You can ignore this issue. Firedrake will still work in parallel, it's just the test harness which is broken. Regards, David On 26/09/2018, 17:33, "firedrake-bounces@imperial.ac.uk on behalf of Yamazaki, Hiroe" <firedrake-bounces@imperial.ac.uk on behalf of h.yamazaki@imperial.ac.uk> wrote: Dear Firedrakers, I am installing firedrake on my macbook Pro with macOS Sierra 10.12.6. With the usual installation procedure (python3 firedrake-install), the installation looks successful (firedrake-install.log attached). However I have got over 200 fails and thousands of warnings in the tests. I have attached some of the error messages (see alltest.log). Do you have any idea how to fix this? All the best, Hiroe
Hi David, That’s a good news. However I still fail the tests on gusto on the same mac which is a problem. I installed gusto using python3 ~/firedrake/bin/firedrake-update --install gusto and it gave some errors (firedrake-update.log attached). I also attached the error messages from the tests on gusto It look like the problem is related to netCDF but I am not sure how to fix it. All the best, Hiroe
On 26 Sep 2018, at 17:35, Ham, David A <david.ham@imperial.ac.uk> wrote:
Dear Hiroe,
This is a known issue on Mac. The parallel test harness is not compatible with OpenMPI 3.0.0. You can ignore this issue. Firedrake will still work in parallel, it's just the test harness which is broken.
Regards,
David
On 26/09/2018, 17:33, "firedrake-bounces@imperial.ac.uk on behalf of Yamazaki, Hiroe" <firedrake-bounces@imperial.ac.uk on behalf of h.yamazaki@imperial.ac.uk> wrote:
Dear Firedrakers,
I am installing firedrake on my macbook Pro with macOS Sierra 10.12.6. With the usual installation procedure (python3 firedrake-install), the installation looks successful (firedrake-install.log attached). However I have got over 200 fails and thousands of warnings in the tests. I have attached some of the error messages (see alltest.log). Do you have any idea how to fix this?
All the best, Hiroe
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi Hiroe, Sorry, we should put some more detailed installation instructions on the Gusto website. This is an extra dependency of Gusto but not of Firedrake. You need to type pip install netCDF4 when inside the Firedrake virtualenv. all the best --Colin ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> Sent: 26 September 2018 17:57:14 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra Hi David, That’s a good news. However I still fail the tests on gusto on the same mac which is a problem. I installed gusto using python3 ~/firedrake/bin/firedrake-update --install gusto and it gave some errors (firedrake-update.log attached). I also attached the error messages from the tests on gusto It look like the problem is related to netCDF but I am not sure how to fix it. All the best, Hiroe
On 26 Sep 2018, at 17:35, Ham, David A <david.ham@imperial.ac.uk> wrote:
Dear Hiroe,
This is a known issue on Mac. The parallel test harness is not compatible with OpenMPI 3.0.0. You can ignore this issue. Firedrake will still work in parallel, it's just the test harness which is broken.
Regards,
David
On 26/09/2018, 17:33, "firedrake-bounces@imperial.ac.uk on behalf of Yamazaki, Hiroe" <firedrake-bounces@imperial.ac.uk on behalf of h.yamazaki@imperial.ac.uk> wrote:
Dear Firedrakers,
I am installing firedrake on my macbook Pro with macOS Sierra 10.12.6. With the usual installation procedure (python3 firedrake-install), the installation looks successful (firedrake-install.log attached). However I have got over 200 fails and thousands of warnings in the tests. I have attached some of the error messages (see alltest.log). Do you have any idea how to fix this?
All the best, Hiroe
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 26 Sep 2018, at 18:02, Cotter, Colin J <colin.cotter@imperial.ac.uk> wrote:
Sorry, we should put some more detailed installation instructions on the Gusto website. This is an extra dependency of Gusto but not of Firedrake. You need to type pip install netCDF4
Something is broken here because gusto specifies netCDF4 inits requirements.txt and firedrake-install is meant to obey that. Lawrence
From what I understood you shouldn’t need to do this if you install gusto in the way that Hiroe did because netCDF4 is in the gusto requirements.txt file - isn’t that the point of that file? Did I misunderstand or did something else go wrong? Jemma ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Cotter, Colin J <colin.cotter@imperial.ac.uk> Sent: 26 September 2018 18:02:39 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra Hi Hiroe, Sorry, we should put some more detailed installation instructions on the Gusto website. This is an extra dependency of Gusto but not of Firedrake. You need to type pip install netCDF4 when inside the Firedrake virtualenv. all the best --Colin ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> Sent: 26 September 2018 17:57:14 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra Hi David, That’s a good news. However I still fail the tests on gusto on the same mac which is a problem. I installed gusto using python3 ~/firedrake/bin/firedrake-update --install gusto and it gave some errors (firedrake-update.log attached). I also attached the error messages from the tests on gusto It look like the problem is related to netCDF but I am not sure how to fix it. All the best, Hiroe
On 26 Sep 2018, at 17:35, Ham, David A <david.ham@imperial.ac.uk> wrote:
Dear Hiroe,
This is a known issue on Mac. The parallel test harness is not compatible with OpenMPI 3.0.0. You can ignore this issue. Firedrake will still work in parallel, it's just the test harness which is broken.
Regards,
David
On 26/09/2018, 17:33, "firedrake-bounces@imperial.ac.uk on behalf of Yamazaki, Hiroe" <firedrake-bounces@imperial.ac.uk on behalf of h.yamazaki@imperial.ac.uk> wrote:
Dear Firedrakers,
I am installing firedrake on my macbook Pro with macOS Sierra 10.12.6. With the usual installation procedure (python3 firedrake-install), the installation looks successful (firedrake-install.log attached). However I have got over 200 fails and thousands of warnings in the tests. I have attached some of the error messages (see alltest.log). Do you have any idea how to fix this?
All the best, Hiroe
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Oh I didn't know about requirements.txt! ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Shipton, Jemma <j.shipton@imperial.ac.uk> Sent: 26 September 2018 18:11:28 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra From what I understood you shouldn’t need to do this if you install gusto in the way that Hiroe did because netCDF4 is in the gusto requirements.txt file - isn’t that the point of that file? Did I misunderstand or did something else go wrong? Jemma ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Cotter, Colin J <colin.cotter@imperial.ac.uk> Sent: 26 September 2018 18:02:39 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra Hi Hiroe, Sorry, we should put some more detailed installation instructions on the Gusto website. This is an extra dependency of Gusto but not of Firedrake. You need to type pip install netCDF4 when inside the Firedrake virtualenv. all the best --Colin ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> Sent: 26 September 2018 17:57:14 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra Hi David, That’s a good news. However I still fail the tests on gusto on the same mac which is a problem. I installed gusto using python3 ~/firedrake/bin/firedrake-update --install gusto and it gave some errors (firedrake-update.log attached). I also attached the error messages from the tests on gusto It look like the problem is related to netCDF but I am not sure how to fix it. All the best, Hiroe
On 26 Sep 2018, at 17:35, Ham, David A <david.ham@imperial.ac.uk> wrote:
Dear Hiroe,
This is a known issue on Mac. The parallel test harness is not compatible with OpenMPI 3.0.0. You can ignore this issue. Firedrake will still work in parallel, it's just the test harness which is broken.
Regards,
David
On 26/09/2018, 17:33, "firedrake-bounces@imperial.ac.uk on behalf of Yamazaki, Hiroe" <firedrake-bounces@imperial.ac.uk on behalf of h.yamazaki@imperial.ac.uk> wrote:
Dear Firedrakers,
I am installing firedrake on my macbook Pro with macOS Sierra 10.12.6. With the usual installation procedure (python3 firedrake-install), the installation looks successful (firedrake-install.log attached). However I have got over 200 fails and thousands of warnings in the tests. I have attached some of the error messages (see alltest.log). Do you have any idea how to fix this?
All the best, Hiroe
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 26 Sep 2018, at 18:02, Cotter, Colin J <colin.cotter@imperial.ac.uk> wrote:
Hi Hiroe, Sorry, we should put some more detailed installation instructions on the Gusto website. This is an extra dependency of Gusto but not of Firedrake. You need to type pip install netCDF4
when inside the Firedrake virtualenv.
all the best --Colin From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> Sent: 26 September 2018 17:57:14 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra
Hi David,
That’s a good news. However I still fail the tests on gusto on the same mac which is a problem. I installed gusto using
python3 ~/firedrake/bin/firedrake-update --install gusto
and it gave some errors (firedrake-update.log attached). I also attached the error messages from the tests on gusto It look like the problem is related to netCDF but I am not sure how to fix it.
All the best, Hiroe
Looking at the update log, it looks like the netCDF4 requirement was correctly picked up, but it failed to install. It looks like this was because there wasn't a wheel available and so it attempted to build from source and couldn't find netcdf and hdf5. I suppose this means we need to build netcdf like we do h5py, but that is painful. Lawrence
Hi all, The problem is solved by doing brew install hdf5 brew install netcdf then inside the Firedrake virtualenv, pip install netcdf4 python3 ~/firedrake/bin/firedrake-update --install gusto Now I pass all the tests on gusto, but still get thousands of warnings. Most of them are: /Users/hiroe/firedrake/src/ufl/ufl/corealg/multifunction.py:31: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() insp = getargspec(function) /Users/hiroe/firedrake/src/COFFEE/coffee/visitor.py:47: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() argspec = inspect.getargspec(meth) I attached the full error message. Do you know how to get rid of these? All the best, Hiroe
On 26 Sep 2018, at 19:04, Lawrence Mitchell <wence@gmx.li> wrote:
On 26 Sep 2018, at 18:02, Cotter, Colin J <colin.cotter@imperial.ac.uk> wrote:
Hi Hiroe, Sorry, we should put some more detailed installation instructions on the Gusto website. This is an extra dependency of Gusto but not of Firedrake. You need to type pip install netCDF4
when inside the Firedrake virtualenv.
all the best --Colin From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> Sent: 26 September 2018 17:57:14 To: firedrake Subject: Re: [firedrake] Installation on macOS Sierra
Hi David,
That’s a good news. However I still fail the tests on gusto on the same mac which is a problem. I installed gusto using
python3 ~/firedrake/bin/firedrake-update --install gusto
and it gave some errors (firedrake-update.log attached). I also attached the error messages from the tests on gusto It look like the problem is related to netCDF but I am not sure how to fix it.
All the best, Hiroe
Looking at the update log, it looks like the netCDF4 requirement was correctly picked up, but it failed to install. It looks like this was because there wasn't a wheel available and so it attempted to build from source and couldn't find netcdf and hdf5. I suppose this means we need to build netcdf like we do h5py, but that is painful.
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 26 Sep 2018, at 20:10, Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> wrote:
Hi all,
The problem is solved by doing
brew install hdf5 brew install netcdf
Although this fixed things, I don't think it is a safe solution, because now netcdf4 is linked against a different hdf5 library to the one installed by petsc (and used by h5py).
then inside the Firedrake virtualenv,
pip install netcdf4 python3 ~/firedrake/bin/firedrake-update --install gusto
Now I pass all the tests on gusto, but still get thousands of warnings. Most of them are:
/Users/hiroe/firedrake/src/ufl/ufl/corealg/multifunction.py:31: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() insp = getargspec(function)
/Users/hiroe/firedrake/src/COFFEE/coffee/visitor.py:47: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() argspec = inspect.getargspec(meth)
I attached the full error message. Do you know how to get rid of these?
This is presumably because your python is so new and shiny (3.7.x). We will have to update COFFEE and UFL to fix them for modern python. These warnings are harmless, but annoying! Lawrence
Hi all, I’ve seen a similar problem building Gusto on Archer. In that case I was able to fix it by pointing the HDF5_DIR and NETCDF4_DIR environment variables at the petsc directory e.g. export HDF5_DIR=/path/to/firedrake/lib/python3.7/site-packages/petsc export NETCDF4_DIR=/path/to/firedrake/lib/python3.7/site-packages/petsc This might work for OS X too? Regards, Dave
On 26 Sep 2018, at 20:16, Lawrence Mitchell <wence@gmx.li> wrote:
On 26 Sep 2018, at 20:10, Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> wrote:
Hi all,
The problem is solved by doing
brew install hdf5 brew install netcdf
Although this fixed things, I don't think it is a safe solution, because now netcdf4 is linked against a different hdf5 library to the one installed by petsc (and used by h5py).
then inside the Firedrake virtualenv,
pip install netcdf4 python3 ~/firedrake/bin/firedrake-update --install gusto
Now I pass all the tests on gusto, but still get thousands of warnings. Most of them are:
/Users/hiroe/firedrake/src/ufl/ufl/corealg/multifunction.py:31: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() insp = getargspec(function)
/Users/hiroe/firedrake/src/COFFEE/coffee/visitor.py:47: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() argspec = inspect.getargspec(meth)
I attached the full error message. Do you know how to get rid of these?
This is presumably because your python is so new and shiny (3.7.x). We will have to update COFFEE and UFL to fix them for modern python. These warnings are harmless, but annoying!
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
I should have said that this uses existing builds of the netCDF and HDF5 libraries from the petsc installation. Both netCDF and HDF5 were built during the petsc installtion on Archer and MacOS so there’s reasonable chance the fix will work for both platforms. Regards, Dave
On 26 Sep 2018, at 21:30, Acreman, David <D.M.Acreman@exeter.ac.uk> wrote:
Hi all,
I’ve seen a similar problem building Gusto on Archer. In that case I was able to fix it by pointing the HDF5_DIR and NETCDF4_DIR environment variables at the petsc directory e.g.
export HDF5_DIR=/path/to/firedrake/lib/python3.7/site-packages/petsc export NETCDF4_DIR=/path/to/firedrake/lib/python3.7/site-packages/petsc
This might work for OS X too?
Regards, Dave
On 26 Sep 2018, at 20:16, Lawrence Mitchell <wence@gmx.li> wrote:
On 26 Sep 2018, at 20:10, Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> wrote:
Hi all,
The problem is solved by doing
brew install hdf5 brew install netcdf
Although this fixed things, I don't think it is a safe solution, because now netcdf4 is linked against a different hdf5 library to the one installed by petsc (and used by h5py).
then inside the Firedrake virtualenv,
pip install netcdf4 python3 ~/firedrake/bin/firedrake-update --install gusto
Now I pass all the tests on gusto, but still get thousands of warnings. Most of them are:
/Users/hiroe/firedrake/src/ufl/ufl/corealg/multifunction.py:31: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() insp = getargspec(function)
/Users/hiroe/firedrake/src/COFFEE/coffee/visitor.py:47: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() argspec = inspect.getargspec(meth)
I attached the full error message. Do you know how to get rid of these?
This is presumably because your python is so new and shiny (3.7.x). We will have to update COFFEE and UFL to fix them for modern python. These warnings are harmless, but annoying!
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
On 26 Sep 2018, at 22:46, Acreman, David <D.M.Acreman@exeter.ac.uk> wrote:
I should have said that this uses existing builds of the netCDF and HDF5 libraries from the petsc installation. Both netCDF and HDF5 were built during the petsc installtion on Archer and MacOS so there’s reasonable chance the fix will work for both platforms.
Yes, I think that's right. We need to figure out how to ensure that this is in the environment appropriately though during firedrake-install. Lawrence
participants (6)
-
Acreman, David
-
Cotter, Colin J
-
Ham, David A
-
Lawrence Mitchell
-
Shipton, Jemma
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Yamazaki, Hiroe