Dear Sir/Madam, I am getting the following netCDF4 error when I try to run Gusto: ---------------------- UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. Traceback (most recent call last): File "examples/sk_nonlinear.py", line 112, in <module> stepper.run(t=0, tmax=tmax) File "/Users/pb412/firedrake/src/gusto/gusto/timeloop.py", line 169, in run state.dump(t, pickup=False) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 345, in dump self.pointdata_output.dump(self.fields, t) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 112, in dump var[idx, :] = vals File "netCDF4/_netCDF4.pyx", line 1908, in netCDF4._netCDF4.Dataset.__exit__ (netCDF4/_netCDF4.c:14289) File "netCDF4/_netCDF4.pyx", line 2012, in netCDF4._netCDF4.Dataset.close (netCDF4/_netCDF4.c:16381) File "netCDF4/_netCDF4.pyx", line 1996, in netCDF4._netCDF4.Dataset._close (netCDF4/_netCDF4.c:16289) File "netCDF4/_netCDF4.pyx", line 1581, in netCDF4._netCDF4._ensure_nc_success (netCDF4/_netCDF4.c:12601) RuntimeError: NetCDF: HDF error -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. ---------------------- There error occurs independent of the model I run (e.g. Rayleigh_Taylor, sk_nonlinear, etc) or the branch I am using (e.g. master, boussinesq_2d_lab, etc). So it seems there is something wrong with the way I have setup the netCDF4 software on my machine...? Please advise what the best way forward is. Regards, Paul
Hi Paul, Could you please tell us what kind of machine (mac laptop?) you're running on and whether you are running in parallel? Thanks! Jemma ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Burns, Paul <P.Burns2@exeter.ac.uk> Sent: 19 September 2017 17:26:56 To: firedrake Subject: [firedrake] netCDF4 error Dear Sir/Madam, I am getting the following netCDF4 error when I try to run Gusto: ---------------------- UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. Traceback (most recent call last): File "examples/sk_nonlinear.py", line 112, in <module> stepper.run(t=0, tmax=tmax) File "/Users/pb412/firedrake/src/gusto/gusto/timeloop.py", line 169, in run state.dump(t, pickup=False) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 345, in dump self.pointdata_output.dump(self.fields, t) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 112, in dump var[idx, :] = vals File "netCDF4/_netCDF4.pyx", line 1908, in netCDF4._netCDF4.Dataset.__exit__ (netCDF4/_netCDF4.c:14289) File "netCDF4/_netCDF4.pyx", line 2012, in netCDF4._netCDF4.Dataset.close (netCDF4/_netCDF4.c:16381) File "netCDF4/_netCDF4.pyx", line 1996, in netCDF4._netCDF4.Dataset._close (netCDF4/_netCDF4.c:16289) File "netCDF4/_netCDF4.pyx", line 1581, in netCDF4._netCDF4._ensure_nc_success (netCDF4/_netCDF4.c:12601) RuntimeError: NetCDF: HDF error -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. ---------------------- There error occurs independent of the model I run (e.g. Rayleigh_Taylor, sk_nonlinear, etc) or the branch I am using (e.g. master, boussinesq_2d_lab, etc). So it seems there is something wrong with the way I have setup the netCDF4 software on my machine...? Please advise what the best way forward is. Regards, Paul
Hi Jemma, Yes it is a Mac, and yes I was running in parallel. Thanks, Paul ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Shipton, Jemma <j.shipton@imperial.ac.uk> Sent: 20 September 2017 14:17:18 To: firedrake Subject: Re: [firedrake] netCDF4 error Hi Paul, Could you please tell us what kind of machine (mac laptop?) you're running on and whether you are running in parallel? Thanks! Jemma ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Burns, Paul <P.Burns2@exeter.ac.uk> Sent: 19 September 2017 17:26:56 To: firedrake Subject: [firedrake] netCDF4 error Dear Sir/Madam, I am getting the following netCDF4 error when I try to run Gusto: ---------------------- UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. Traceback (most recent call last): File "examples/sk_nonlinear.py", line 112, in <module> stepper.run(t=0, tmax=tmax) File "/Users/pb412/firedrake/src/gusto/gusto/timeloop.py", line 169, in run state.dump(t, pickup=False) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 345, in dump self.pointdata_output.dump(self.fields, t) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 112, in dump var[idx, :] = vals File "netCDF4/_netCDF4.pyx", line 1908, in netCDF4._netCDF4.Dataset.__exit__ (netCDF4/_netCDF4.c:14289) File "netCDF4/_netCDF4.pyx", line 2012, in netCDF4._netCDF4.Dataset.close (netCDF4/_netCDF4.c:16381) File "netCDF4/_netCDF4.pyx", line 1996, in netCDF4._netCDF4.Dataset._close (netCDF4/_netCDF4.c:16289) File "netCDF4/_netCDF4.pyx", line 1581, in netCDF4._netCDF4._ensure_nc_success (netCDF4/_netCDF4.c:12601) RuntimeError: NetCDF: HDF error -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. ---------------------- There error occurs independent of the model I run (e.g. Rayleigh_Taylor, sk_nonlinear, etc) or the branch I am using (e.g. master, boussinesq_2d_lab, etc). So it seems there is something wrong with the way I have setup the netCDF4 software on my machine...? Please advise what the best way forward is. Regards, Paul
Hi Paul, Could you please send the output of `firedrake-status` command? Also, I presume you have write access to the directory where gusto tries to write the outputs? NetCDF/hdf5 errors are not often very informative. Does gusto work in serial? Regards, Tuomas On 09/20/2017 06:41 AM, Burns, Paul wrote:
Hi Jemma,
Yes it is a Mac, and yes I was running in parallel.
Thanks,
Paul
------------------------------------------------------------------------ *From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Shipton, Jemma <j.shipton@imperial.ac.uk> *Sent:* 20 September 2017 14:17:18 *To:* firedrake *Subject:* Re: [firedrake] netCDF4 error
Hi Paul,
Could you please tell us what kind of machine (mac laptop?) you're running on and whether you are running in parallel?
Thanks!
Jemma
------------------------------------------------------------------------ *From:* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Burns, Paul <P.Burns2@exeter.ac.uk> *Sent:* 19 September 2017 17:26:56 *To:* firedrake *Subject:* [firedrake] netCDF4 error
Dear Sir/Madam,
I am getting the following netCDF4 error when I try to run Gusto:
----------------------
UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element.
UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element.
Traceback (most recent call last):
File "examples/sk_nonlinear.py", line 112, in <module>
stepper.run(t=0, tmax=tmax)
File "/Users/pb412/firedrake/src/gusto/gusto/timeloop.py", line 169, in run
state.dump(t, pickup=False)
File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 345, in dump
self.pointdata_output.dump(self.fields, t)
File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 112, in dump
var[idx, :] = vals
File "netCDF4/_netCDF4.pyx", line 1908, in netCDF4._netCDF4.Dataset.__exit__ (netCDF4/_netCDF4.c:14289)
File "netCDF4/_netCDF4.pyx", line 2012, in netCDF4._netCDF4.Dataset.close (netCDF4/_netCDF4.c:16381)
File "netCDF4/_netCDF4.pyx", line 1996, in netCDF4._netCDF4.Dataset._close (netCDF4/_netCDF4.c:16289)
File "netCDF4/_netCDF4.pyx", line 1581, in netCDF4._netCDF4._ensure_nc_success (netCDF4/_netCDF4.c:12601)
RuntimeError: NetCDF: HDF error
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
----------------------
There error occurs independent of the model I run (e.g. Rayleigh_Taylor, sk_nonlinear, etc) or the branch I am using (e.g. master, boussinesq_2d_lab, etc). So it seems there is something wrong with the way I have setup the netCDF4 software on my machine...?
Please advise what the best way forward is.
Regards,
Paul
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi, It appears to be running now in both serial and parallel after I updated the computer's Xcode software. Regards, Paul ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Tuomas Karna <tuomas.karna@gmail.com> Sent: 20 September 2017 16:45:38 To: firedrake@imperial.ac.uk Subject: Re: [firedrake] netCDF4 error Hi Paul, Could you please send the output of `firedrake-status` command? Also, I presume you have write access to the directory where gusto tries to write the outputs? NetCDF/hdf5 errors are not often very informative. Does gusto work in serial? Regards, Tuomas On 09/20/2017 06:41 AM, Burns, Paul wrote: Hi Jemma, Yes it is a Mac, and yes I was running in parallel. Thanks, Paul ________________________________ From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk><mailto:firedrake-bounces@imperial.ac.uk> on behalf of Shipton, Jemma <j.shipton@imperial.ac.uk><mailto:j.shipton@imperial.ac.uk> Sent: 20 September 2017 14:17:18 To: firedrake Subject: Re: [firedrake] netCDF4 error Hi Paul, Could you please tell us what kind of machine (mac laptop?) you're running on and whether you are running in parallel? Thanks! Jemma ________________________________ From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk><mailto:firedrake-bounces@imperial.ac.uk> on behalf of Burns, Paul <P.Burns2@exeter.ac.uk><mailto:P.Burns2@exeter.ac.uk> Sent: 19 September 2017 17:26:56 To: firedrake Subject: [firedrake] netCDF4 error Dear Sir/Madam, I am getting the following netCDF4 error when I try to run Gusto: ---------------------- UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. UFL:WARNING Discontinuous Lagrange element requested on interval * interval, creating DQ element. Traceback (most recent call last): File "examples/sk_nonlinear.py", line 112, in <module> stepper.run(t=0, tmax=tmax) File "/Users/pb412/firedrake/src/gusto/gusto/timeloop.py", line 169, in run state.dump(t, pickup=False) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 345, in dump self.pointdata_output.dump(self.fields, t) File "/Users/pb412/firedrake/src/gusto/gusto/state.py", line 112, in dump var[idx, :] = vals File "netCDF4/_netCDF4.pyx", line 1908, in netCDF4._netCDF4.Dataset.__exit__ (netCDF4/_netCDF4.c:14289) File "netCDF4/_netCDF4.pyx", line 2012, in netCDF4._netCDF4.Dataset.close (netCDF4/_netCDF4.c:16381) File "netCDF4/_netCDF4.pyx", line 1996, in netCDF4._netCDF4.Dataset._close (netCDF4/_netCDF4.c:16289) File "netCDF4/_netCDF4.pyx", line 1581, in netCDF4._netCDF4._ensure_nc_success (netCDF4/_netCDF4.c:12601) RuntimeError: NetCDF: HDF error -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. ---------------------- There error occurs independent of the model I run (e.g. Rayleigh_Taylor, sk_nonlinear, etc) or the branch I am using (e.g. master, boussinesq_2d_lab, etc). So it seems there is something wrong with the way I have setup the netCDF4 software on my machine...? Please advise what the best way forward is. Regards, Paul _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (3)
-
Burns, Paul
-
Shipton, Jemma
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Tuomas Karna