Hi Sjors,
We compiled Relion 1.3 in the TACC Lonestar using intel compiler 11.1. It
went through with some warnings.
There was no fatal error. Could you please check the feupdateenv in
particular?
Thanks.
Qiu-Xing
‹‹‹
login2$ ./INSTALL.sh -j 8
Compiling fftw-3.2.2 ...
See /work/00982/jiangq99/relion-1.3/external/fftw_build.log for details
Compiling fltk-1.3.0 ...
See /work/00982/jiangq99/relion-1.3/external/fltk_build.log for details
configure: WARNING: Ignoring libraries " -lSM -lICE" requested by
configure.
Compiling relion ...
See /work/00982/jiangq99/relion-1.3/relion_build.log for details
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
src/assembly.cpp(356): warning #181: argument is incompatible with
corresponding format string conversion
atomnum, molecules[imol].residues[ires].atoms[iatom].name.c_str(),
molecules[imol].residues[ires].name.c_str(),
^
src/args.cpp(104): warning #1011: missing return statement at end of
non-void function "IOParser::operator="
}
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 206 of "src/ctffind_runner.cpp"
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 206 of "src/ctffind_runner.cpp"
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 117 of "src/autopicker.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 769 of "src/exp_model.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
src/filename.cpp(316): warning #68: integer conversion resulted in a
change of sign
if ( find("#", 0) > -1 )
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 132 of "src/ml_model.cpp"
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 1123 of "src/ml_optimiser.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.
h")
double log2(double value);
^
src/parallel.cpp(271): warning #186: pointless comparison of unsigned
integer with zero
if (tasks < 0 || tasks >= numberOfTasks)
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 128 of
"src/particle_polisher.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 92 of "src/particle_sorter.cpp"
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 102 of "src/postprocessing.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 447 of "src/preprocessing.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
src/time.cpp(223): warning #1011: missing return statement at end of
non-void function "Timer::toc"
}
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 314 of
"src/particle_polisher_mpi.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 1369 of
"src/ml_optimiser_mpi.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/displayer.h(327): warning #1011: missing return statement at end of
non-void function "popupInputWindow::fill"
}
^
src/displayer.cpp(221): warning #1011: missing return statement at end of
non-void function "basisViewerWindow::fillCanvas"
}
^
src/displayer.cpp(412): warning #1011: missing return statement at end of
non-void function "basisViewerCanvas::fill(MetaDataTable &, EMDLabel,
bool, double, double, double, double, int)"
}
^
src/displayer.cpp(429): warning #1011: missing return statement at end of
non-void function "basisViewerCanvas::fill(MultidimArray<double> &,
double, double, double, double)"
}
^
src/displayer.cpp(1848): warning #1011: missing return statement at end of
non-void function "Displayer::runGui"
}
^
src/displayer.cpp(1964): warning #1011: missing return statement at end of
non-void function "Displayer::run"
}
^
./src/image.h(598): warning #1011: missing return statement at end of
non-void function "Image<T>::checkMmapT"
}
^
detected during:
instantiation of "int Image<T>::readData(FILE *, long,
DataType={DataType}, unsigned long) [with T=double]" at line 246 of
"./src/rwSPIDER.h"
instantiation of "int Image<T>::readSPIDER(long) [with
T=double]" at line 1157
instantiation of "int Image<T>::_read(const FileName &,
fImageHandler *, bool, long, bool, bool) [with T=double]" at line 256
instantiation of "int Image<T>::read(const FileName &, bool,
long, bool, bool) [with T=double]" at line 176 of "src/displayer.cpp"
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
./src/funcs.h(301): warning #584: omission of exception specification is
incompatible with previous function "log2" (declared at line 145 of
"/usr/include/bits/mathcalls.h")
double log2(double value);
^
/opt/apps/intel/11.1/lib/intel64/libimf.so/opt/apps/intel/11.1/lib/intel64/
libimf.so/opt/apps/intel/11.1/lib/intel64/libimf.so:
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so:: warning: warning: feupdateenv
is not implemented and will always fail :warning: warning: feupdateenv is
not implemented and will always failwarning:
warning: feupdateenv is not implemented and will always fail
warning: warning: feupdateenv is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
/opt/apps/intel/11.1/lib/intel64/libimf.so: warning: warning: feupdateenv
is not implemented and will always fail
Done!
------
On 10/17/14, 4:50 AM, "Sjors Scheres" <[log in to unmask]> wrote:
>How big are the images? How many movie frames does each image have? What
>are the command line arguments of the job that crashes?
>S
>
>On 10/17/2014 08:53 AM, SUBSCRIBE CCPEM SIddhanta wrote:
>> Hi all,
>>
>> I am new to Relion. I have been following the tutorial closely to
>>process around 12000 particles. Processing is done on a cluster (details
>>given below). At almost every job (mainly for movie processing) we have
>>faced memory issues or other problems which are causing the program to
>>crash. However, after extensive trial and error with the cluster admin,
>>we managed to find optimum settings for MPI processes and threads for
>>each job.
>>
>> Unfortunately, now in particle polishing none of the configurations are
>>working. I've tried many. It mostly exits with the error 'segmentation
>>fault' at the particle writing stage or some times with
>>'std:bad_alloc()' right at the beginning.
>>
>> Cluster details: 8 nodes, each with 64 cores and 128 GB ram.
>>
>> I'm giving a little extra info which might help in trouble shooting.
>>(these are all for movie processing)
>> Optimal settings determined for
>>
>> 3D Classification: 128 MPI processes, 4 threads, 2 GB per thread
>> 3D Auto refine: 32 MPI processes, 16 threads, 2 GB per thread
>>
>> For particle polishing, I've tried everything, from 8 MPI and 32
>>threads to 32 MPI and 4 threads. They all return with segmentation
>>fault. And higher settings than 32 MPI or lower than 8 MPI cause the
>>program to crash immediately.
>>
>> I hope I can get some help on this. Thanks in advance.
>
>--
>Sjors Scheres
>MRC Laboratory of Molecular Biology
>Francis Crick Avenue, Cambridge Biomedical Campus
>Cambridge CB2 0QH, U.K.
>tel: +44 (0)1223 267061
>http://www2.mrc-lmb.cam.ac.uk/groups/scheres
________________________________
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