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precice / systemtests

Testing preCICE / solver combinations using Docker
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Unexpected end of /proc/mounts line local_test Ubuntu 16.04 #187

Open fsimonis opened 4 years ago

fsimonis commented 4 years ago

Open MPI fails to parse /proc/mounts in docker containers.

Unexpected end of /proc/mounts line `overlay / overlay rw,relatime,lowerdir=/work_fast/docker/overlay2/l/LSSTTVRAJFQKCH2EL7TQVVWNE3:/work_fast/docker/overlay2/l/E7SVFSB2LOQJGXPCGQCHO5K6SH:/work_fast/docker/overlay2/l/L7U5E72OZD4B4LZKEHIWZGCE3U:/work_fast/docker/overlay2/l/Y3SYJIFHIFOAQWJ3LFON6MG7ZV:/work_fast/docker/overlay2/l/OZ73REB4NO3ABTCYS5SSBKZJW5:/work_fast/docker/overlay2/l/NWNNQ7LIB7ORFKU2WSLHKOYW25:/work_fast/docker/overlay2/l/VTXPAOYTUU37HUCNW4TDB366FA:/work_fast/docker/overlay2/l/ORNABTXUGD45GN72M7TYCLKNBA:/work_fast/docker/overla'
Unexpected end of /proc/mounts line `y2/l/JBC52A3KAYFS5IGDSAQZEQDZWA:/work_fast/docker/overlay2/l/6RX7WB6SBCX45SZGJPKRAJTGXS:/work_fast/docker/overlay2/l/PQB5NLGOFB55TALSFQBK677G2R:/work_fast/docker/overlay2/l/OD4ZGRBVUPHR72PNT7PSHBXMEP:/work_fast/docker/overlay2/l/JXXTOUPWYSD7ERRBBOCMLSNIMT:/work_fast/docker/overlay2/l/K3UIJ7TRKKNAHFP7B73AOKNT6E:/work_fast/docker/overlay2/l/DNMY6ES6VFNGCCHXC3YRIXX7CF:/work_fast/docker/overlay2/l/HY7I5VKZ7NETM2ELRL2TXHH5FL:/work_fast/docker/overlay2/l/WOCT4SDQFU3FUL2KQYY422BV74:/work_fast/docker/overlay2/l/FS'
Unexpected end of /proc/mounts line `Q632SSW7MNLZBM34IYA3NFXM:/work_fast/docker/overlay2/l/RQQIBQPL4XPU46MYTYYY6HCFC4:/work_fast/docker/overlay2/l/FSZQCOMJ7OQDWB2MXJY4FV5W6P:/work_fast/docker/overlay2/l/347YFWCIEAUKI343NA523HAITN:/work_fast/docker/overlay2/l/FCFHPBRAIRJPB4TNYDFYHBY3CG:/work_fast/docker/overlay2/l/F7OOHA44URRVMIUHXVZU6SBQX6:/work_fast/docker/overlay2/l/65QQ5EWZASWNX5FSIWOQWXSSHQ:/work_fast/docker/overlay2/l/4KCZ6ODKL54DGJOPU76BKY2URH:/work_fast/docker/overlay2/l/XSNUIMBARL236HC5ARDQHBDRSG:/work_fast/docker/overlay2/l/GDGOS634G'
Unexpected end of /proc/mounts line `overlay / overlay rw,relatime,lowerdir=/work_fast/docker/overlay2/l/LSSTTVRAJFQKCH2EL7TQVVWNE3:/work_fast/docker/overlay2/l/E7SVFSB2LOQJGXPCGQCHO5K6SH:/work_fast/docker/overlay2/l/L7U5E72OZD4B4LZKEHIWZGCE3U:/work_fast/docker/overlay2/l/Y3SYJIFHIFOAQWJ3LFON6MG7ZV:/work_fast/docker/overlay2/l/OZ73REB4NO3ABTCYS5SSBKZJW5:/work_fast/docker/overlay2/l/NWNNQ7LIB7ORFKU2WSLHKOYW25:/work_fast/docker/overlay2/l/VTXPAOYTUU37HUCNW4TDB366FA:/work_fast/docker/overlay2/l/ORNABTXUGD45GN72M7TYCLKNBA:/work_fast/docker/overla'
Unexpected end of /proc/mounts line `y2/l/JBC52A3KAYFS5IGDSAQZEQDZWA:/work_fast/docker/overlay2/l/6RX7WB6SBCX45SZGJPKRAJTGXS:/work_fast/docker/overlay2/l/PQB5NLGOFB55TALSFQBK677G2R:/work_fast/docker/overlay2/l/OD4ZGRBVUPHR72PNT7PSHBXMEP:/work_fast/docker/overlay2/l/JXXTOUPWYSD7ERRBBOCMLSNIMT:/work_fast/docker/overlay2/l/K3UIJ7TRKKNAHFP7B73AOKNT6E:/work_fast/docker/overlay2/l/DNMY6ES6VFNGCCHXC3YRIXX7CF:/work_fast/docker/overlay2/l/HY7I5VKZ7NETM2ELRL2TXHH5FL:/work_fast/docker/overlay2/l/WOCT4SDQFU3FUL2KQYY422BV74:/work_fast/docker/overlay2/l/FS'
Unexpected end of /proc/mounts line `Q632SSW7MNLZBM34IYA3NFXM:/work_fast/docker/overlay2/l/RQQIBQPL4XPU46MYTYYY6HCFC4:/work_fast/docker/overlay2/l/FSZQCOMJ7OQDWB2MXJY4FV5W6P:/work_fast/docker/overlay2/l/347YFWCIEAUKI343NA523HAITN:/work_fast/docker/overlay2/l/FCFHPBRAIRJPB4TNYDFYHBY3CG:/work_fast/docker/overlay2/l/F7OOHA44URRVMIUHXVZU6SBQX6:/work_fast/docker/overlay2/l/65QQ5EWZASWNX5FSIWOQWXSSHQ:/work_fast/docker/overlay2/l/4KCZ6ODKL54DGJOPU76BKY2URH:/work_fast/docker/overlay2/l/XSNUIMBARL236HC5ARDQHBDRSG:/work_fast/docker/overlay2/l/GDGOS634G

Reason why can b found here:

This is likely due to your /proc/mount file having a line in it greater than 512 characters, causing the hwloc module of OpenMPI to fail to parse it correctly. Docker has a tendency to put very long lines into /proc/mounts.

And a possible solution here:

This issue should be fixed in hwloc since 1.11.3 (released 2 years ago). You can either upgrade to OpenMPI 3.0 which contains a hwloc 1.11.7 >= 1.11.3. Or recompile OpenMPI to use an external hwloc instead of the old embedded one.