data not initialized - Githubissues

aymeric-spiga / dynamico-giant

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data not initialized #5

Closed alboiss closed 5 years ago

alboiss commented 5 years ago

3D dynamico runs stop approximately 10 seconds after they begin. I get the following error (message from proc 19 is sent by everyone):

00: Remapping... 19: > Error [template void CType::checkEmpty(void) const] : In file '/scratch/cnt0027/lmd1167/aboissinot/dynamico-giant/code/XIOS/src/attribute_template_impl.hpp', line 78 -> On checking attribute with id=operation : data is not initialized 19: 19: 19: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 19 00: slurmstepd: STEP 5202504.0 ON n1668 CANCELLED AT 2018-09-27T11:37:30 srun: Job step aborted: Waiting up to 32 seconds for job step to finish. srun: error: n1668: tasks 0-19: Killed srun: Terminating job step 5202504.0 srun: error: n1675: tasks 20-39: Killed

aymeric-spiga commented 5 years ago

Does it work with version https://github.com/aymeric-spiga/dynamico-giant/commit/6058e908dbd5f3499c4ec72adf1014b7e10a58d7

aymeric-spiga commented 5 years ago

(no need to recompile, I mean version of XML and def in dynamico-giant version indicated above)

alboiss commented 5 years ago

It doesn't work with version 6058e90 (same error message).

aymeric-spiga commented 5 years ago

I am having the same problem trying to launch a job_mpi in makestart

> Error [template <typename T> void CType<T>::checkEmpty(void) const] : In file '/scratch/cnt0027/lmd1167/aspigaplaneto/dynamico-giant/code/XIOS/src/type/type_impl.hpp', line 210 -> Data is not initialized

aymeric-spiga commented 5 years ago

Using

##############
### CONFIG ###
ver_dyn=687 # ICOSAGCM
ver_phys=1911 # ARCH ICOSA_LMDZ LMDZ.COMMON LMDZ.GENERIC
ver_xios=1459 # XIOS
ver_ioipsl=302 # IOIPSL
##############

aymeric-spiga commented 5 years ago

With HEAD same problem

Error [template <typename T> void CType<T>::checkEmpty(void) const] : In file '/scratch/cnt0027/lmd1167/aspigaplaneto/dynamico-giant/code/XIOS/src/attribute_template_impl.hpp', line 78 -> On checking attribute with id=operation : data is not initialized

aymeric-spiga commented 5 years ago

@ehouarn : works for Saturn 32 levels with dynamico-giant https://github.com/aymeric-spiga/dynamico-giant/commit/e9a6f98b7d07b64ac94a76f1e939912c7254dd68 and HEAD in install.sh

aymeric-spiga commented 5 years ago

BUT with following changes

dissipation fields were missing from field_def.xml (to be committed)
icosa.xml to output dyn and dissip (done at later commit already)
iodef.xml is not in server mode <variable id="using_server" type="bool">false</variable>
run_icosa.def change in write_period (done at later commit already)
run_icosa.def replace scheme by time_scheme = ARK2.3

aymeric-spiga commented 5 years ago

OK so I just tested with https://github.com/aymeric-spiga/dynamico-giant/commit/26da5a54120ce4c73decdad9519e81b5167e06a2 Looks like @ehouarn commit https://github.com/aymeric-spiga/dynamico-giant/commit/928e8968858381d5e1f36640acf19ad6f2b7b275 solves the problem Could you check @alboiss?

aymeric-spiga commented 5 years ago

Well that did not fully work. I am getting a SEG FAULT!

aymeric-spiga commented 5 years ago

I am going to close this issue because this has been solved. And either open a new one, or relate to an existing issue.