Hello Zhichao, sorry for the long delay, I got started on other work and forgot about this email.
You should not need to install Ubuntu from scratch as Cactus should run in a docker container (Steve Brandt tests this before each release). You may want to try and set a couple of extra environment variables before you run the code: export OMPI_MCA_btl_vader_single_copy_mechanism="none" which at one point prevented (harmless) warnings for me when running in a (modern) Ubuntu container (old ones were fine). Can you tell me what image you are running inside of the container, please? I would like to try it out and see if this is what is causing problems for you. It also turns out I could have already given you a better (though not really helpful) answer before. Your errors are: 83bdcfc58a2e:55616] Read -1, expected 31752, errno = 1 meaning a read failed (31752 bytes were supposed to be read but none were read) and the error number (errno) was 1. Running this through the strerror function (part of C but also eg in the python posix.strerror code: python -c 'import posix; print (posix.strerror(1))' which returns "Operation not permitted". Normally this would be a file that cannot be read from, though the only file your code reads is the LORENE data file for the initial data, which results in a different error when it cannot be opened, so I am still stumped. Yours, Roland > Thank you Dr. Roland, > > In fact the parfile I used is NsNsToHMNS.par > <https://einsteintoolkit.org/gallery/bns/nsnstohmns.par>(click to open > hyperlink). I just changed the Initial Data file. > However, when I trying to use another parfiles, for example, > BBHHighRes.par, the error also occurs. > > 83bdcfc58a2e is the identification of this machine (this node), so I guess > it is something wrong with Docker ( I run ET in a docker ) ? > > I have upload an err file generated by simfactory(located in > ~/simfactory/bbh/output-0000/bbh.err). > > Maybe I should reinstall my OS to ubuntu and then run ET without docker ? > > Thanks again for your help. > > Yours, > Zhichao. > > > > Haas, Roland <[email protected]> 于2019年9月10日周二 下午8:14写道： > > > Hello ZhiChao, > > > > > > + date +%s > > > > + export CACTUS_STARTTIME=1567761511 > > > > + [ 14 = 1 ] > > > > + mpirun -np 14 > > /home/zhaozc/simulations/bnstest/SIMFACTORY/exe/cactus_sim > > > > -L 3 /home/zhaozc/simulations/bnstest /output-0000/bnstest.par > > > > [83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19027] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19029] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19024] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19026] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19028] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19032] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19034] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19036] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19030] Read -1, expected 4096, errno = 1 > > > > [83bdcfc58a2e:19023] Read -1, expected 4096, errno = 1 > > > > > > ...... > > > > > > > > > but those errors will not terminate the task. > > > Is it safe to ignore those errors? > > Would you mind providing the parfile bnstest.par that you are running, > > please? It does not seem to exist in the Einstein Toolkit repos and > > without it all we can do is guess what could be happening. > > > > The string "Read.*expected" also does not seem to show up anywhere in > > my Cactus tree (or any of my executables for that matter), so that I am > > not sure at all which thorn or module is even generating this error. > > > > The string does however show up in libgfortran.so so that I would guess > > that it is some Fortran code not checking if it could open a file > > correctly. > > > > You can try running what looks like an address: 83bdcfc58a2e through > > the addr2line command: > > > > addr2line -e /home/zhaozc/simulations/bnstest/SIMFACTORY/exe/cactus_sim > > 0x83bdcfc58a2e > > > > or use gdb: > > > > gdb /home/zhaozc/simulations/bnstest/SIMFACTORY/exe/cactus_sim > > info line *0x83bdcfc58a2e > > > > to try and find out which thorn was responsible, though I cannot > > guarantee that this will work. > > > > A blind guess would be that some thorn fails to open a file, does not > > properly check for this and then find that it cannot read anything from > > that (not opened file) in which case eg the read() system call returns > > -1. > > > > Yours, > > Roland > > > > -- > > My email is as private as my paper mail. I therefore support encrypting > > and signing email messages. Get my PGP key from http://pgp.mit.edu . > > > > -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .
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