[Users] Err logs like "[83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1" when running ET.

[Haas, Roland]

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 <rhaas at illinois.edu> 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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