problems with EMAN installation in UBUNTU 11 and errors with windows version
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Wouter Van Putte
Feb 14, 2012, 10:57:19 AM2/14/12
to EMAN2
Hello,
I have just started to work with EMAN2. First I tried to work with the
windows version, but I had problems in the sense that I could not use
the generate output function in the particle section. The error that
appears is that the commandline is too long. I have a total of 400
images, so that might be the reason, but I don't know how to solve
this. However, I could circumvent this problem by using the write
output in the select particle section. But now I also have problems
with the CTF function. The problem there is that once I've calculated
the structure factor, I could not go back to autofitting and the
tuning section. I could only calculate the structure factor when I
selected only a small part of my particles.
After these problems I thought the linux version would be more stable,
but now I seem to have problems with the installation. The error I get
is (python:2112): Gtk-WARNING **: Kan themamodule niet vinden in
modulepad: ‘pixmap’ (in english this means it can't find back the
thememodule in modulepath: "pixmap").
I hope some-one can explain me how I can solve this. I am using the
latest Ubuntu 11 as OS.
Best regards,
Wouter
I have just started to work with EMAN2. First I tried to work with the
windows version, but I had problems in the sense that I could not use
the generate output function in the particle section. The error that
appears is that the commandline is too long. I have a total of 400
images, so that might be the reason, but I don't know how to solve
this. However, I could circumvent this problem by using the write
output in the select particle section. But now I also have problems
with the CTF function. The problem there is that once I've calculated
the structure factor, I could not go back to autofitting and the
tuning section. I could only calculate the structure factor when I
selected only a small part of my particles.
After these problems I thought the linux version would be more stable,
but now I seem to have problems with the installation. The error I get
is (python:2112): Gtk-WARNING **: Kan themamodule niet vinden in
modulepad: ‘pixmap’ (in english this means it can't find back the
thememodule in modulepath: "pixmap").
I hope some-one can explain me how I can solve this. I am using the
latest Ubuntu 11 as OS.
Best regards,
Wouter
Grant Tang
Feb 14, 2012, 11:14:02 AM2/14/12
to em...@googlegroups.com
Hi, Wouter:
What version of Ubuntu 11 you have? 64 bit or 32 bit?
What installer file you used to install EMAN2?
What command you run to cause this error message?
Grant
Grant Tang
Feb 14, 2012, 12:39:53 PM2/14/12
to em...@googlegroups.com
Hi, Wouter:
Is the error message means:
Gtk-WARNING **: Unable to locate theme engine in module_path: "pixmap"
It's a warning message you can ignore. Or you can fix it by running
following command:
sudo apt-get install gtk2-engines-pixbuf
Grant
On Tue, 2012-02-14 at 09:57 -0600, Wouter Van Putte wrote:
Wouter Van Putte
Feb 17, 2012, 8:55:26 AM2/17/12
to EMAN2
hello Grant,
sorry for my late response. But for the moment things are working even
better then when I was using it for windows. So thanks a lot.
Best regards,
Wouter
sorry for my late response. But for the moment things are working even
better then when I was using it for windows. So thanks a lot.
Best regards,
Wouter
Wouter Van Putte
Feb 19, 2012, 1:47:57 PM2/19/12
to EMAN2
Hello Grant,
I've got a new problem... The calculation of the initial defocus
values of part I of the CTF heading works (it writes down two files),
but then something goes wrong in the sense that I can't continue with
correcting the CTF estimation as part II doesn't pop up. The error
message I get is "segmentation fault". Any clue on how I can solve
this? I am also not able to rerun the first step of the CTF or any
other function of the CTF.
Best regards,
Wouter
I've got a new problem... The calculation of the initial defocus
values of part I of the CTF heading works (it writes down two files),
but then something goes wrong in the sense that I can't continue with
correcting the CTF estimation as part II doesn't pop up. The error
message I get is "segmentation fault". Any clue on how I can solve
this? I am also not able to rerun the first step of the CTF or any
other function of the CTF.
Best regards,
Wouter
Wouter Van Putte
Feb 19, 2012, 2:15:50 PM2/19/12
to EMAN2
some extra information:
ubuntu 11.1
7.7Gb, Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8 , 64-bit
eman src 2.04
so automated fitting (CTF) works, but after that I get the
"Segmentation fault" when I try to start Interactive Tuning
I hope this helps
W
ubuntu 11.1
7.7Gb, Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8 , 64-bit
eman src 2.04
so automated fitting (CTF) works, but after that I get the
"Segmentation fault" when I try to start Interactive Tuning
I hope this helps
W
Steven Ludtke
Feb 19, 2012, 2:18:05 PM2/19/12
to em...@googlegroups.com
Hi Wouter. What version of EMAN2 do you have ? (run e2version.py)
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
Co-Director National Center For Macromolecular Imaging ARE
Baylor College of Medicine The converse
slu...@bcm.edu -or- ste...@alumni.caltech.edu also applies
http://ncmi.bcm.edu/~stevel
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
Co-Director National Center For Macromolecular Imaging ARE
Baylor College of Medicine The converse
slu...@bcm.edu -or- ste...@alumni.caltech.edu also applies
http://ncmi.bcm.edu/~stevel
> --
> ----------------------------------------------------------------------------------------------
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Wouter Van Putte
Feb 19, 2012, 2:23:26 PM2/19/12
to EMAN2
EMAN 2.0.4 (CVS 2011/11/17 18:07:45)
On 19 feb, 20:18, Steven Ludtke <sludtk...@gmail.com> wrote:
> Hi Wouter. What version of EMAN2 do you have ? (run e2version.py)
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
Steven Ludtke
Feb 19, 2012, 2:42:06 PM2/19/12
to em...@googlegroups.com
This sort of segfault generally indicates some oddity in the images you're trying to process. Of course, it should not crash, even if there is some issue with the images, so it may well be something that's been fixed since (ie - so it produces a readable error message, or handles the images in some special way). While I'd be happy to help you through the debugging process if you like, the easiest thing to try first would be to install a current snapshot version of EMAN2 and see if that corrects the problem...
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
Co-Director National Center For Macromolecular Imaging ARE
Baylor College of Medicine The converse
slu...@bcm.edu -or- ste...@alumni.caltech.edu also applies
http://ncmi.bcm.edu/~stevel
Wouter Van Putte
Feb 19, 2012, 3:26:40 PM2/19/12
to EMAN2
thank you for the help,
I'll try the snapshot version...
best regards
Wouter
On 19 feb, 20:42, Steven Ludtke <sludtk...@gmail.com> wrote:
> This sort of segfault generally indicates some oddity in the images you're trying to process. Of course, it should not crash, even if there is some issue with the images, so it may well be something that's been fixed since (ie - so it produces a readable error message, or handles the images in some special way). While I'd be happy to help you through the debugging process if you like, the easiest thing to try first would be to install a current snapshot version of EMAN2 and see if that corrects the problem...
>
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
> slud...@bcm.edu -or- ste...@alumni.caltech.edu also applieshttp://ncmi.bcm.edu/~stevel
I'll try the snapshot version...
best regards
Wouter
On 19 feb, 20:42, Steven Ludtke <sludtk...@gmail.com> wrote:
> This sort of segfault generally indicates some oddity in the images you're trying to process. Of course, it should not crash, even if there is some issue with the images, so it may well be something that's been fixed since (ie - so it produces a readable error message, or handles the images in some special way). While I'd be happy to help you through the debugging process if you like, the easiest thing to try first would be to install a current snapshot version of EMAN2 and see if that corrects the problem...
>
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
>
> On Feb 19, 2012, at 1:18 PM, Steven Ludtke wrote:
>
>
>
>
>
>
>
> > Hi Wouter. What version of EMAN2 do you have ? (run e2version.py)
> > ----------------------------------------------------------------------------
> > Steven Ludtke, Ph.D.
> > Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> > Co-Director National Center For Macromolecular Imaging ARE
> > Baylor College of Medicine The converse
> > slud...@bcm.edu -or- ste...@alumni.caltech.edu also applies
> On Feb 19, 2012, at 1:18 PM, Steven Ludtke wrote:
>
>
>
>
>
>
>
> > Hi Wouter. What version of EMAN2 do you have ? (run e2version.py)
> > ----------------------------------------------------------------------------
> > Steven Ludtke, Ph.D.
> > Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> > Co-Director National Center For Macromolecular Imaging ARE
> > Baylor College of Medicine The converse
Wouter Van Putte
Feb 19, 2012, 4:08:52 PM2/19/12
to EMAN2
I just installed the daily version, but the problem is still there...
this is what I'v egot
object libEM/CMakeFiles/EM2.dir/boxingtools.o
[ 2%] Building CXX object libEM/CMakeFiles/EM2.dir/util.o
[ 3%] Building CXX object libEM/CMakeFiles/EM2.dir/emutil.o
[ 3%] Building CXX object libEM/CMakeFiles/EM2.dir/pointarray.o
[ 4%] Building CXX object libEM/CMakeFiles/EM2.dir/pdbreader.o
[ 6%] Building CXX object libEM/CMakeFiles/EM2.dir/hdfio2.o
[ 7%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata.o
[ 7%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_io.o
[ 8%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_core.o
[ 9%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_cuda.o
[ 10%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_modular.o
[ 12%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_metadata.o
[ 12%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_transform.o
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::bispecRotTransInvN(int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1170:7: let
op: variable ‘kIx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp: In
memberfunctie ‘EMAN::EMData*
EMAN::EMData::bispecRotTransInvDirect(int)’:
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1630:34: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1748:34: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::bispecRotTransInvN(int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1138:28: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1139:29: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
[ 13%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
emdata_sparx.o
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::FH2F(int, float, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:312:8: let
op: variable ‘kValue’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::FourTruncate(int, int, int,
bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:6940:27: let
op: variable ‘inx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::Four_ds(int, int, int,
bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7143:27: let
op: variable ‘inx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7143:32: let
op: variable ‘iny’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7143:37: let
op: variable ‘inz’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::Four_shuf_ds_cen_us(int,
int, int, bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7192:27: let
op: variable ‘inx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7192:32: let
op: variable ‘iny’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7192:37: let
op: variable ‘inz’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData*
EMAN::EMData::replace_amplitudes(EMAN::EMData*, bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7333:6: let
op: variable ‘nox’ set but not used [-Wunused-but-set-variable]
[ 14%] Building CXX object libEM/CMakeFiles/EM2.dir/ctf.o
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp: In memberfunctie ‘virtual
std::vector<float> EMAN::EMAN2Ctf::compute_1d(int, float,
EMAN::Ctf::CtfType, EMAN::XYData*)’:
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp:788:10: let op: variable
‘bg’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp: In memberfunctie ‘virtual
void EMAN::EMAN2Ctf::compute_2d_complex(EMAN::EMData*,
EMAN::Ctf::CtfType, EMAN::XYData*)’:
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp:955:11: let op: variable
‘bg’ set but not used [-Wunused-but-set-variable]
[ 15%] Building CXX object libEM/CMakeFiles/EM2.dir/processor.o
/home/wouter/EMAN2/src/eman2/libEM/processor.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::Wiener2DAutoAreaProcessor::process(const
EMAN::EMData*)’:
/home/wouter/EMAN2/src/eman2/libEM/processor.cpp:1051:9: let op:
variable ‘fftd’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/processor.cpp:1052:6: let op:
variable ‘f’ set but not used [-Wunused-but-set-variable]
[ 15%] Building CXX object libEM/CMakeFiles/EM2.dir/aligner.o
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::RotationalAligner::align(EMAN::EMData*,
EMAN::EMData*, const string&, const EMAN::Dict&) const’:
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp:336:8: let op: variable
‘score’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::RefineAligner::align(EMAN::EMData*,
EMAN::EMData*, const string&, const EMAN::Dict&) const’:
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp:1471:8: let op:
variable ‘sscale’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp: In functie ‘float
{anonymous}::frm_2d_Align(EMAN::EMData*, EMAN::EMData*, float*,
EMAN::EMData*, int, int, float&, float&, float&, float&, const
string&, const EMAN::Dict&)’:
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp:2529:16: let op:
variable ‘index0’ set but not used [-Wunused-but-set-variable]
[ 17%] Building CXX object libEM/CMakeFiles/EM2.dir/projector.o
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘int EMAN::ChaoProjector::sph2cb(float*, EMAN::Vec3i, int, int, int,
int*, int*, float*) const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1367:15: let op:
variable ‘r2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘int EMAN::ChaoProjector::bckpj3(EMAN::Vec3i, int, int, float*,
EMAN::Vec3i, int, int*, int*, float*, float*) const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1479:31: let op:
variable ‘dx1m’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1479:37: let op:
variable ‘dy1m’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::ChaoProjector::project3d(EMAN::EMData*)
const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1605:18: let op:
variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘virtual EMAN::EMData*
EMAN::ChaoProjector::backproject3d(EMAN::EMData*) const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1723:18: let op:
variable ‘status’ set but not used [-Wunused-but-set-variable]
[ 18%] Building CXX object libEM/CMakeFiles/EM2.dir/cmp.o
[ 19%] Building CXX object libEM/CMakeFiles/EM2.dir/averager.o
[ 20%] Building CXX object libEM/CMakeFiles/EM2.dir/reconstructor.o
[ 20%] Building CXX object libEM/CMakeFiles/EM2.dir/
reconstructor_tools.o
[ 21%] Building CXX object libEM/CMakeFiles/EM2.dir/testutil.o
[ 23%] Building CXX object libEM/CMakeFiles/EM2.dir/analyzer.o
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp: In memberfunctie
‘virtual std::vector<EMAN::EMData*> EMAN::PCAsmall::analyze()’:
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp:278:6: let op:
variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp: In memberfunctie ‘int
EMAN::PCAlarge::Lanczos(const string&, int*, float*, float*, float*,
float*)’:
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp:585:50: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp:616:54: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
[ 23%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
fundamentals.o
[ 24%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
fourierfilter.o
[ 25%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
rsconvolution.o
[ 26%] Building CXX object libEM/CMakeFiles/EM2.dir/polardata.o
[ 28%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/util_sparx.o
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::fftc_d(double*, double*, int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:2627:34: let
op: variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::fftc_q(float*, float*, int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:2786:6: let
op: variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static EMAN::Dict
EMAN::Util::Crosrng_sm_psi(EMAN::EMData*, EMAN::EMData*,
std::vector<int>, float, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:3972:31: let
op: variable ‘qm’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:3972:41: let
op: variable ‘tmt’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static EMAN::Dict EMAN::Util::coveig_for_py(int,
const std::vector<float>&)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6379:6: let
op: variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static std::vector<float>
EMAN::Util::pw_extract(std::vector<float>, int, int, float)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6416:10: let
op: variable ‘n1’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6416:44: let
op: variable ‘n2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::cl1(long int*, long int*,
long int*, long int*, long int*, double*, double*, double*, double*,
long int*, double*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6676:18: let
op: variable ‘error’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::voronoi(double*, double*,
double*, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:7661:31: let
op: variable ‘mdup’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘double areav_new__(int*, int*, double*, double*, double*, int*, int*,
int*, int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:9137:18: let
op: variable ‘areav’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int drwarc_(int*, double*, double*, double*, int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:11451:22: let
op: variable ‘p1’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int trlprt_(int*, double*, double*, double*, int*, int*, int*, int*,
int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:15358:24: let
op: variable ‘na’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int trplot_(int*, double*, double*, double*, double*, int*, double*,
double*, double*, int*, int*, int*, char*, long int*, int*, short
int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16056:35: let
op: variable ‘tx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16056:39: let
op: variable ‘ty’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16059:22: let
op: variable ‘ipx2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16059:34: let
op: variable ‘ipy2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int trprnt_(int*, double*, double*, double*, int*, int*, int*, int*,
int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16535:19: let
op: variable ‘na’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16535:43: let
op: variable ‘nt’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16535:68: let
op: variable ‘nabor’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int vrplot_(int*, double*, double*, double*, double*, int*, double*,
double*, double*, int*, int*, int*, int*, double*, double*, double*,
char*, long int*, int*, short int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16849:35: let
op: variable ‘tx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16849:39: let
op: variable ‘ty’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16853:22: let
op: variable ‘ipx2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16853:34: let
op: variable ‘ipy2’ set but not used [-Wunused-but-set-variable]
[ 29%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/pca.o
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp: In memberfunctie
‘int EMAN::PCA::Lanczos_ooc(const string&, int*, float*, float*, const
string&, float*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp:588:48: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp:599:48: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp: In memberfunctie
‘int EMAN::PCA::dopca_ooc(const string&, const string&, const string&,
EMAN::EMData*, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp:263:46: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
[ 30%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/steepest.o
[ 30%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/
volume_data.o
[ 31%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/volume.o
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp: In memberfunctie
‘int wustl_mm::SkeletonMaker::Volume::hasCompleteHelix(int, int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp:1462:8: let op:
variable ‘j’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp: In memberfunctie
‘int wustl_mm::SkeletonMaker::Volume::hasCompleteHelix(int, int, int,
wustl_mm::SkeletonMaker::Volume*)’:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp:1518:8: let op:
variable ‘j’ set but not used [-Wunused-but-set-variable]
In file included from /home/wouter/EMAN2/src/eman2/libEM/gorgon/
volume.h:12:0,
from /home/wouter/EMAN2/src/eman2/libEM/gorgon/
volume.cpp:5:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/priority_queue.h: In
memberfunctie ‘void EMAN::PriorityQueue<ValueT,
KeyT>::remove(ValueT*&, KeyT&) [with ValueT =
wustl_mm::SkeletonMaker::gridPoint, KeyT = int]’:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp:4078:31:
instantiated from here
/home/wouter/EMAN2/src/eman2/libEM/gorgon/priority_queue.h:185:3: let
op: converting to non-pointer type ‘int’ from NULL [-Wconversion-null]
[ 32%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/
skeletonizer.o
Linking CXX shared library ../lib/libEM2.so
[ 75%] Built target EM2
Scanning dependencies of target GLEM2
[ 76%] Building CXX object libEM/CMakeFiles/GLEM2.dir/glutil.o
/home/wouter/EMAN2/src/eman2/libEM/glutil.cpp: In static member
function ‘static std::string EMAN::GLUtil::render_amp8(EMAN::EMData*,
int, int, int, int, int, float, int, int, float, float, float, int)’:
/home/wouter/EMAN2/src/eman2/libEM/glutil.cpp:464:52: let op: ‘ph’ may
be used uninitialized in this function [-Wuninitialized]
/home/wouter/EMAN2/src/eman2/libEM/glutil.cpp:395:52: let op: ‘ph’ may
be used uninitialized in this function [-Wuninitialized]
[ 78%] Building CXX object libEM/CMakeFiles/GLEM2.dir/marchingcubes.o
Linking CXX shared library ../lib/libGLEM2.so
[ 78%] Built target GLEM2
Scanning dependencies of target pyAligner2
[ 79%] Building CXX object libpyEM/CMakeFiles/pyAligner2.dir/
libpyAligner2.o
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
Linking CXX shared library ../lib/libpyAligner2.so
[ 79%] Built target pyAligner2
Scanning dependencies of target pyAnalyzer2
[ 80%] Building CXX object libpyEM/CMakeFiles/pyAnalyzer2.dir/
libpyAnalyzer2.o
Linking CXX shared library ../lib/libpyAnalyzer2.so
[ 80%] Built target pyAnalyzer2
Scanning dependencies of target pyAverager2
[ 80%] Building CXX object libpyEM/CMakeFiles/pyAverager2.dir/
libpyAverager2.o
Linking CXX shared library ../lib/libpyAverager2.so
[ 80%] Built target pyAverager2
Scanning dependencies of target pyBoxingTools2
[ 81%] Building CXX object libpyEM/CMakeFiles/pyBoxingTools2.dir/
libpyBoxingTools2.o
Linking CXX shared library ../lib/libpyBoxingTools2.so
[ 81%] Built target pyBoxingTools2
Scanning dependencies of target pyCmp2
[ 82%] Building CXX object libpyEM/CMakeFiles/pyCmp2.dir/libpyCmp2.o
Linking CXX shared library ../lib/libpyCmp2.so
[ 82%] Built target pyCmp2
Scanning dependencies of target pyEMData2
[ 84%] Building CXX object libpyEM/CMakeFiles/pyEMData2.dir/
libpyEMData2.o
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
[ 85%] Building CXX object libpyEM/CMakeFiles/pyEMData2.dir/
emdata_wrapitems.o
Linking CXX shared library ../lib/libpyEMData2.so
[ 85%] Built target pyEMData2
Scanning dependencies of target pyEMObject2
[ 85%] Building CXX object libpyEM/CMakeFiles/pyEMObject2.dir/
libpyEMObject2.o
Linking CXX shared library ../lib/libpyEMObject2.so
[ 85%] Built target pyEMObject2
Scanning dependencies of target pyFundamentals2
[ 86%] Building CXX object libpyEM/CMakeFiles/pyFundamentals2.dir/
libpyFundamentals2.o
Linking CXX shared library ../lib/libpyFundamentals2.so
[ 86%] Built target pyFundamentals2
Scanning dependencies of target pyGLUtils2
[ 87%] Building CXX object libpyEM/CMakeFiles/pyGLUtils2.dir/
libpyGLUtils2.o
Linking CXX shared library ../lib/libpyGLUtils2.so
[ 87%] Built target pyGLUtils2
Linking CXX shared library ../lib/libpyGeometry2.so
[ 89%] Built target pyGeometry2
Scanning dependencies of target pyMarchingCubes2
[ 90%] Building CXX object libpyEM/CMakeFiles/pyMarchingCubes2.dir/
libpyMarchingCubes2.o
Linking CXX shared library ../lib/libpyMarchingCubes2.so
[ 90%] Built target pyMarchingCubes2
Scanning dependencies of target pyPDBReader2
[ 90%] Building CXX object libpyEM/CMakeFiles/pyPDBReader2.dir/
libpyPDBReader2.o
Linking CXX shared library ../lib/libpyPDBReader2.so
[ 90%] Built target pyPDBReader2
Scanning dependencies of target pyPointArray2
[ 91%] Building CXX object libpyEM/CMakeFiles/pyPointArray2.dir/
libpyPointArray2.o
Linking CXX shared library ../lib/libpyPointArray2.so
[ 91%] Built target pyPointArray2
Scanning dependencies of target pyPolarData2
[ 92%] Building CXX object libpyEM/CMakeFiles/pyPolarData2.dir/
libpyPolarData2.o
Linking CXX shared library ../lib/libpyPolarData2.so
[ 92%] Built target pyPolarData2
Scanning dependencies of target pyProcessor2
[ 93%] Building CXX object libpyEM/CMakeFiles/pyProcessor2.dir/
libpyProcessor2.o
Linking CXX shared library ../lib/libpyProcessor2.so
[ 93%] Built target pyProcessor2
Scanning dependencies of target pyProjector2
[ 93%] Building CXX object libpyEM/CMakeFiles/pyProjector2.dir/
libpyProjector2.o
Linking CXX shared library ../lib/libpyProjector2.so
[ 93%] Built target pyProjector2
Scanning dependencies of target pyReconstructor2
[ 95%] Building CXX object libpyEM/CMakeFiles/pyReconstructor2.dir/
libpyReconstructor2.o
Linking CXX shared library ../lib/libpyReconstructor2.so
[ 95%] Built target pyReconstructor2
Scanning dependencies of target pyTransform2
[ 96%] Building CXX object libpyEM/CMakeFiles/pyTransform2.dir/
libpyTransform2.o
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
Linking CXX shared library ../lib/libpyTransform2.so
[ 96%] Built target pyTransform2
Scanning dependencies of target pyTypeConverter2
[ 97%] Building CXX object libpyEM/CMakeFiles/pyTypeConverter2.dir/
libpyTypeConverter2.o
[ 98%] Building CXX object libpyEM/CMakeFiles/pyTypeConverter2.dir/
typeconverter.o
Linking CXX shared library ../lib/libpyTypeConverter2.so
[ 98%] Built target pyTypeConverter2
Scanning dependencies of target pyUtils2
[ 98%] Building CXX object libpyEM/CMakeFiles/pyUtils2.dir/
libpyUtils2.o
/home/wouter/EMAN2/src/eman2/libpyEM/libpyUtils2.cpp: In functie ‘void
readarray(boost::python::api::object&, boost::python::numeric::array&,
int)’:
/home/wouter/EMAN2/src/eman2/libpyEM/libpyUtils2.cpp:329:41: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/usr/include/python2.7/numpy/__multiarray_api.h: At global scope:
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
Linking CXX shared library ../lib/libpyUtils2.so
[ 98%] Built target pyUtils2
Scanning dependencies of target e2speedtest
[100%] Building CXX object utils/CMakeFiles/e2speedtest.dir/
speedtest.o
Linking CXX executable ../bin/e2speedtest
[100%] Built target e2speedtest
I've checked the particles and then I tried to regenerate the output,
but this time it runs really slow in comparison to the previous time
and I also don't see anything happening in the running tasks.
so the problems are still there...
I'll continue working on it tomorrow morning
best regards,
this is what I'v egot
object libEM/CMakeFiles/EM2.dir/boxingtools.o
[ 2%] Building CXX object libEM/CMakeFiles/EM2.dir/util.o
[ 3%] Building CXX object libEM/CMakeFiles/EM2.dir/emutil.o
[ 3%] Building CXX object libEM/CMakeFiles/EM2.dir/pointarray.o
[ 4%] Building CXX object libEM/CMakeFiles/EM2.dir/pdbreader.o
[ 6%] Building CXX object libEM/CMakeFiles/EM2.dir/hdfio2.o
[ 7%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata.o
[ 7%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_io.o
[ 8%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_core.o
[ 9%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_cuda.o
[ 10%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_modular.o
[ 12%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_metadata.o
[ 12%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_transform.o
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::bispecRotTransInvN(int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1170:7: let
op: variable ‘kIx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp: In
memberfunctie ‘EMAN::EMData*
EMAN::EMData::bispecRotTransInvDirect(int)’:
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1630:34: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1748:34: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::bispecRotTransInvN(int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1138:28: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/emdata_transform.cpp:1139:29: let
op: ignoring return value of ‘int system(const char*)’, declared with
attribute warn_unused_result [-Wunused-result]
[ 13%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
emdata_sparx.o
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::FH2F(int, float, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:312:8: let
op: variable ‘kValue’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::FourTruncate(int, int, int,
bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:6940:27: let
op: variable ‘inx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::Four_ds(int, int, int,
bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7143:27: let
op: variable ‘inx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7143:32: let
op: variable ‘iny’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7143:37: let
op: variable ‘inz’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData* EMAN::EMData::Four_shuf_ds_cen_us(int,
int, int, bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7192:27: let
op: variable ‘inx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7192:32: let
op: variable ‘iny’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7192:37: let
op: variable ‘inz’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp: In
memberfunctie ‘EMAN::EMData*
EMAN::EMData::replace_amplitudes(EMAN::EMData*, bool)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:7333:6: let
op: variable ‘nox’ set but not used [-Wunused-but-set-variable]
[ 14%] Building CXX object libEM/CMakeFiles/EM2.dir/ctf.o
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp: In memberfunctie ‘virtual
std::vector<float> EMAN::EMAN2Ctf::compute_1d(int, float,
EMAN::Ctf::CtfType, EMAN::XYData*)’:
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp:788:10: let op: variable
‘bg’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp: In memberfunctie ‘virtual
void EMAN::EMAN2Ctf::compute_2d_complex(EMAN::EMData*,
EMAN::Ctf::CtfType, EMAN::XYData*)’:
/home/wouter/EMAN2/src/eman2/libEM/ctf.cpp:955:11: let op: variable
‘bg’ set but not used [-Wunused-but-set-variable]
[ 15%] Building CXX object libEM/CMakeFiles/EM2.dir/processor.o
/home/wouter/EMAN2/src/eman2/libEM/processor.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::Wiener2DAutoAreaProcessor::process(const
EMAN::EMData*)’:
/home/wouter/EMAN2/src/eman2/libEM/processor.cpp:1051:9: let op:
variable ‘fftd’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/processor.cpp:1052:6: let op:
variable ‘f’ set but not used [-Wunused-but-set-variable]
[ 15%] Building CXX object libEM/CMakeFiles/EM2.dir/aligner.o
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::RotationalAligner::align(EMAN::EMData*,
EMAN::EMData*, const string&, const EMAN::Dict&) const’:
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp:336:8: let op: variable
‘score’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::RefineAligner::align(EMAN::EMData*,
EMAN::EMData*, const string&, const EMAN::Dict&) const’:
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp:1471:8: let op:
variable ‘sscale’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp: In functie ‘float
{anonymous}::frm_2d_Align(EMAN::EMData*, EMAN::EMData*, float*,
EMAN::EMData*, int, int, float&, float&, float&, float&, const
string&, const EMAN::Dict&)’:
/home/wouter/EMAN2/src/eman2/libEM/aligner.cpp:2529:16: let op:
variable ‘index0’ set but not used [-Wunused-but-set-variable]
[ 17%] Building CXX object libEM/CMakeFiles/EM2.dir/projector.o
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘int EMAN::ChaoProjector::sph2cb(float*, EMAN::Vec3i, int, int, int,
int*, int*, float*) const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1367:15: let op:
variable ‘r2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘int EMAN::ChaoProjector::bckpj3(EMAN::Vec3i, int, int, float*,
EMAN::Vec3i, int, int*, int*, float*, float*) const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1479:31: let op:
variable ‘dx1m’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1479:37: let op:
variable ‘dy1m’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘virtual EMAN::EMData* EMAN::ChaoProjector::project3d(EMAN::EMData*)
const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1605:18: let op:
variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp: In memberfunctie
‘virtual EMAN::EMData*
EMAN::ChaoProjector::backproject3d(EMAN::EMData*) const’:
/home/wouter/EMAN2/src/eman2/libEM/projector.cpp:1723:18: let op:
variable ‘status’ set but not used [-Wunused-but-set-variable]
[ 18%] Building CXX object libEM/CMakeFiles/EM2.dir/cmp.o
[ 19%] Building CXX object libEM/CMakeFiles/EM2.dir/averager.o
[ 20%] Building CXX object libEM/CMakeFiles/EM2.dir/reconstructor.o
[ 20%] Building CXX object libEM/CMakeFiles/EM2.dir/
reconstructor_tools.o
[ 21%] Building CXX object libEM/CMakeFiles/EM2.dir/testutil.o
[ 23%] Building CXX object libEM/CMakeFiles/EM2.dir/analyzer.o
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp: In memberfunctie
‘virtual std::vector<EMAN::EMData*> EMAN::PCAsmall::analyze()’:
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp:278:6: let op:
variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp: In memberfunctie ‘int
EMAN::PCAlarge::Lanczos(const string&, int*, float*, float*, float*,
float*)’:
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp:585:50: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/analyzer.cpp:616:54: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
[ 23%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
fundamentals.o
[ 24%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
fourierfilter.o
[ 25%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/
rsconvolution.o
[ 26%] Building CXX object libEM/CMakeFiles/EM2.dir/polardata.o
[ 28%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/util_sparx.o
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::fftc_d(double*, double*, int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:2627:34: let
op: variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::fftc_q(float*, float*, int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:2786:6: let
op: variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static EMAN::Dict
EMAN::Util::Crosrng_sm_psi(EMAN::EMData*, EMAN::EMData*,
std::vector<int>, float, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:3972:31: let
op: variable ‘qm’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:3972:41: let
op: variable ‘tmt’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static EMAN::Dict EMAN::Util::coveig_for_py(int,
const std::vector<float>&)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6379:6: let
op: variable ‘status’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static std::vector<float>
EMAN::Util::pw_extract(std::vector<float>, int, int, float)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6416:10: let
op: variable ‘n1’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6416:44: let
op: variable ‘n2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::cl1(long int*, long int*,
long int*, long int*, long int*, double*, double*, double*, double*,
long int*, double*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:6676:18: let
op: variable ‘error’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In static
member function ‘static void EMAN::Util::voronoi(double*, double*,
double*, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:7661:31: let
op: variable ‘mdup’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘double areav_new__(int*, int*, double*, double*, double*, int*, int*,
int*, int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:9137:18: let
op: variable ‘areav’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int drwarc_(int*, double*, double*, double*, int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:11451:22: let
op: variable ‘p1’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int trlprt_(int*, double*, double*, double*, int*, int*, int*, int*,
int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:15358:24: let
op: variable ‘na’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int trplot_(int*, double*, double*, double*, double*, int*, double*,
double*, double*, int*, int*, int*, char*, long int*, int*, short
int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16056:35: let
op: variable ‘tx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16056:39: let
op: variable ‘ty’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16059:22: let
op: variable ‘ipx2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16059:34: let
op: variable ‘ipy2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int trprnt_(int*, double*, double*, double*, int*, int*, int*, int*,
int*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16535:19: let
op: variable ‘na’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16535:43: let
op: variable ‘nt’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16535:68: let
op: variable ‘nabor’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp: In functie
‘int vrplot_(int*, double*, double*, double*, double*, int*, double*,
double*, double*, int*, int*, int*, int*, double*, double*, double*,
char*, long int*, int*, short int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16849:35: let
op: variable ‘tx’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16849:39: let
op: variable ‘ty’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16853:22: let
op: variable ‘ipx2’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/sparx/util_sparx.cpp:16853:34: let
op: variable ‘ipy2’ set but not used [-Wunused-but-set-variable]
[ 29%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/pca.o
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp: In memberfunctie
‘int EMAN::PCA::Lanczos_ooc(const string&, int*, float*, float*, const
string&, float*)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp:588:48: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp:599:48: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp: In memberfunctie
‘int EMAN::PCA::dopca_ooc(const string&, const string&, const string&,
EMAN::EMData*, int)’:
/home/wouter/EMAN2/src/eman2/libEM/sparx/pca.cpp:263:46: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
[ 30%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/steepest.o
[ 30%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/
volume_data.o
[ 31%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/volume.o
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp: In memberfunctie
‘int wustl_mm::SkeletonMaker::Volume::hasCompleteHelix(int, int,
int)’:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp:1462:8: let op:
variable ‘j’ set but not used [-Wunused-but-set-variable]
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp: In memberfunctie
‘int wustl_mm::SkeletonMaker::Volume::hasCompleteHelix(int, int, int,
wustl_mm::SkeletonMaker::Volume*)’:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp:1518:8: let op:
variable ‘j’ set but not used [-Wunused-but-set-variable]
In file included from /home/wouter/EMAN2/src/eman2/libEM/gorgon/
volume.h:12:0,
from /home/wouter/EMAN2/src/eman2/libEM/gorgon/
volume.cpp:5:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/priority_queue.h: In
memberfunctie ‘void EMAN::PriorityQueue<ValueT,
KeyT>::remove(ValueT*&, KeyT&) [with ValueT =
wustl_mm::SkeletonMaker::gridPoint, KeyT = int]’:
/home/wouter/EMAN2/src/eman2/libEM/gorgon/volume.cpp:4078:31:
instantiated from here
/home/wouter/EMAN2/src/eman2/libEM/gorgon/priority_queue.h:185:3: let
op: converting to non-pointer type ‘int’ from NULL [-Wconversion-null]
[ 32%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/
skeletonizer.o
Linking CXX shared library ../lib/libEM2.so
[ 75%] Built target EM2
Scanning dependencies of target GLEM2
[ 76%] Building CXX object libEM/CMakeFiles/GLEM2.dir/glutil.o
/home/wouter/EMAN2/src/eman2/libEM/glutil.cpp: In static member
function ‘static std::string EMAN::GLUtil::render_amp8(EMAN::EMData*,
int, int, int, int, int, float, int, int, float, float, float, int)’:
/home/wouter/EMAN2/src/eman2/libEM/glutil.cpp:464:52: let op: ‘ph’ may
be used uninitialized in this function [-Wuninitialized]
/home/wouter/EMAN2/src/eman2/libEM/glutil.cpp:395:52: let op: ‘ph’ may
be used uninitialized in this function [-Wuninitialized]
[ 78%] Building CXX object libEM/CMakeFiles/GLEM2.dir/marchingcubes.o
Linking CXX shared library ../lib/libGLEM2.so
[ 78%] Built target GLEM2
Scanning dependencies of target pyAligner2
[ 79%] Building CXX object libpyEM/CMakeFiles/pyAligner2.dir/
libpyAligner2.o
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
Linking CXX shared library ../lib/libpyAligner2.so
[ 79%] Built target pyAligner2
Scanning dependencies of target pyAnalyzer2
[ 80%] Building CXX object libpyEM/CMakeFiles/pyAnalyzer2.dir/
libpyAnalyzer2.o
Linking CXX shared library ../lib/libpyAnalyzer2.so
[ 80%] Built target pyAnalyzer2
Scanning dependencies of target pyAverager2
[ 80%] Building CXX object libpyEM/CMakeFiles/pyAverager2.dir/
libpyAverager2.o
Linking CXX shared library ../lib/libpyAverager2.so
[ 80%] Built target pyAverager2
Scanning dependencies of target pyBoxingTools2
[ 81%] Building CXX object libpyEM/CMakeFiles/pyBoxingTools2.dir/
libpyBoxingTools2.o
Linking CXX shared library ../lib/libpyBoxingTools2.so
[ 81%] Built target pyBoxingTools2
Scanning dependencies of target pyCmp2
[ 82%] Building CXX object libpyEM/CMakeFiles/pyCmp2.dir/libpyCmp2.o
Linking CXX shared library ../lib/libpyCmp2.so
[ 82%] Built target pyCmp2
Scanning dependencies of target pyEMData2
[ 84%] Building CXX object libpyEM/CMakeFiles/pyEMData2.dir/
libpyEMData2.o
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
[ 85%] Building CXX object libpyEM/CMakeFiles/pyEMData2.dir/
emdata_wrapitems.o
Linking CXX shared library ../lib/libpyEMData2.so
[ 85%] Built target pyEMData2
Scanning dependencies of target pyEMObject2
[ 85%] Building CXX object libpyEM/CMakeFiles/pyEMObject2.dir/
libpyEMObject2.o
Linking CXX shared library ../lib/libpyEMObject2.so
[ 85%] Built target pyEMObject2
Scanning dependencies of target pyFundamentals2
[ 86%] Building CXX object libpyEM/CMakeFiles/pyFundamentals2.dir/
libpyFundamentals2.o
Linking CXX shared library ../lib/libpyFundamentals2.so
[ 86%] Built target pyFundamentals2
Scanning dependencies of target pyGLUtils2
[ 87%] Building CXX object libpyEM/CMakeFiles/pyGLUtils2.dir/
libpyGLUtils2.o
Linking CXX shared library ../lib/libpyGLUtils2.so
[ 87%] Built target pyGLUtils2
Linking CXX shared library ../lib/libpyGeometry2.so
[ 89%] Built target pyGeometry2
Scanning dependencies of target pyMarchingCubes2
[ 90%] Building CXX object libpyEM/CMakeFiles/pyMarchingCubes2.dir/
libpyMarchingCubes2.o
Linking CXX shared library ../lib/libpyMarchingCubes2.so
[ 90%] Built target pyMarchingCubes2
Scanning dependencies of target pyPDBReader2
[ 90%] Building CXX object libpyEM/CMakeFiles/pyPDBReader2.dir/
libpyPDBReader2.o
Linking CXX shared library ../lib/libpyPDBReader2.so
[ 90%] Built target pyPDBReader2
Scanning dependencies of target pyPointArray2
[ 91%] Building CXX object libpyEM/CMakeFiles/pyPointArray2.dir/
libpyPointArray2.o
Linking CXX shared library ../lib/libpyPointArray2.so
[ 91%] Built target pyPointArray2
Scanning dependencies of target pyPolarData2
[ 92%] Building CXX object libpyEM/CMakeFiles/pyPolarData2.dir/
libpyPolarData2.o
Linking CXX shared library ../lib/libpyPolarData2.so
[ 92%] Built target pyPolarData2
Scanning dependencies of target pyProcessor2
[ 93%] Building CXX object libpyEM/CMakeFiles/pyProcessor2.dir/
libpyProcessor2.o
Linking CXX shared library ../lib/libpyProcessor2.so
[ 93%] Built target pyProcessor2
Scanning dependencies of target pyProjector2
[ 93%] Building CXX object libpyEM/CMakeFiles/pyProjector2.dir/
libpyProjector2.o
Linking CXX shared library ../lib/libpyProjector2.so
[ 93%] Built target pyProjector2
Scanning dependencies of target pyReconstructor2
[ 95%] Building CXX object libpyEM/CMakeFiles/pyReconstructor2.dir/
libpyReconstructor2.o
Linking CXX shared library ../lib/libpyReconstructor2.so
[ 95%] Built target pyReconstructor2
Scanning dependencies of target pyTransform2
[ 96%] Building CXX object libpyEM/CMakeFiles/pyTransform2.dir/
libpyTransform2.o
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
Linking CXX shared library ../lib/libpyTransform2.so
[ 96%] Built target pyTransform2
Scanning dependencies of target pyTypeConverter2
[ 97%] Building CXX object libpyEM/CMakeFiles/pyTypeConverter2.dir/
libpyTypeConverter2.o
[ 98%] Building CXX object libpyEM/CMakeFiles/pyTypeConverter2.dir/
typeconverter.o
Linking CXX shared library ../lib/libpyTypeConverter2.so
[ 98%] Built target pyTypeConverter2
Scanning dependencies of target pyUtils2
[ 98%] Building CXX object libpyEM/CMakeFiles/pyUtils2.dir/
libpyUtils2.o
/home/wouter/EMAN2/src/eman2/libpyEM/libpyUtils2.cpp: In functie ‘void
readarray(boost::python::api::object&, boost::python::numeric::array&,
int)’:
/home/wouter/EMAN2/src/eman2/libpyEM/libpyUtils2.cpp:329:41: let op:
ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’,
declared with attribute warn_unused_result [-Wunused-result]
/usr/include/python2.7/numpy/__multiarray_api.h: At global scope:
/usr/include/python2.7/numpy/__multiarray_api.h:1187:1: let op: ‘int
_import_array()’ defined but not used [-Wunused-function]
Linking CXX shared library ../lib/libpyUtils2.so
[ 98%] Built target pyUtils2
Scanning dependencies of target e2speedtest
[100%] Building CXX object utils/CMakeFiles/e2speedtest.dir/
speedtest.o
Linking CXX executable ../bin/e2speedtest
[100%] Built target e2speedtest
I've checked the particles and then I tried to regenerate the output,
but this time it runs really slow in comparison to the previous time
and I also don't see anything happening in the running tasks.
so the problems are still there...
I'll continue working on it tomorrow morning
best regards,
> This sort of segfault generally indicates some oddity in the images you're trying to process. Of course, it should not crash, even if there is some issue with the images, so it may well be something that's been fixed since (ie - so it produces a readable error message, or handles the images in some special way). While I'd be happy to help you through the debugging process if you like, the easiest thing to try first would be to install a current snapshot version of EMAN2 and see if that corrects the problem...
>
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
> slud...@bcm.edu -or- ste...@alumni.caltech.edu also applieshttp://ncmi.bcm.edu/~stevel
>
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
>
> On Feb 19, 2012, at 1:18 PM, Steven Ludtke wrote:
>
>
>
>
>
>
>
> > Hi Wouter. What version of EMAN2 do you have ? (run e2version.py)
> > ----------------------------------------------------------------------------
> > Steven Ludtke, Ph.D.
> > Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> > Co-Director National Center For Macromolecular Imaging ARE
> > Baylor College of Medicine The converse
> > slud...@bcm.edu -or- ste...@alumni.caltech.edu also applies
> On Feb 19, 2012, at 1:18 PM, Steven Ludtke wrote:
>
>
>
>
>
>
>
> > Hi Wouter. What version of EMAN2 do you have ? (run e2version.py)
> > ----------------------------------------------------------------------------
> > Steven Ludtke, Ph.D.
> > Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> > Co-Director National Center For Macromolecular Imaging ARE
> > Baylor College of Medicine The converse
Steven Ludtke
Feb 19, 2012, 9:34:29 PM2/19/12
to em...@googlegroups.com
You're compiling from source rather than using a binary ? That's fine, of course, but you should make sure you have all of the correct options set in ccmake to get optimal performance. Here are my current Linux options:
ENABLE_ATHLON OFF
ENABLE_AUTODOC OFF
ENABLE_BOUNDS_CHECKING OFF
ENABLE_DEBUG OFF
ENABLE_EMAN_CUDA OFF
ENABLE_FFTW2 OFF
ENABLE_FFTW3 ON
ENABLE_FFTW_PLAN_CACHING ON
ENABLE_FTGL ON
ENABLE_HDF5 ON
ENABLE_IOCACHE OFF
ENABLE_JPEG ON
ENABLE_LEOPARD OFF
ENABLE_MEMDEBUG OFF
ENABLE_MEMDEBUG2 OFF
ENABLE_NATIVE_FFT OFF
ENABLE_NFFT2 OFF
ENABLE_OPENGL ON
ENABLE_OPTPP OFF
ENABLE_PNG ON
ENABLE_PROFILE OFF
ENABLE_RT ON
ENABLE_SPARX_CUDA OFF
ENABLE_TIFF ON
ENABLE_V4L2 OFF
ENABLE_X86_64 ON
Anyway, that's just with respect to the speed, not the crash. For the crash, probably the easiest thing to do, if you're willing, is to pass me the HDF file you're trying to run e2initialmodel.py on, and see if I can replicate the crash. If you have a little more hackerish background, I can send you some instructions explaining how to figure out what's causing the segfault...
If you want to send the file and it's too big to email, you can use https://bigfile.bcm.edu/
Sorry you're running into issues :^(
----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
Co-Director National Center For Macromolecular Imaging ARE
Baylor College of Medicine The converse
slu...@bcm.edu -or- ste...@alumni.caltech.edu also applies
http://ncmi.bcm.edu/~stevel
Wouter Van Putte
Feb 20, 2012, 7:25:59 AM2/20/12
to EMAN2
I also have these:
//If build EMAN with libftgl.a
ENABLE_STATIC_FTGL:BOOL=OFF
//enable TAO support
ENABLE_TAO:BOOL=OFF
ok?
For the rest everything was the same except : ENABLE_X86_64, so I
changed into ON
> If you want to send the file and it's too big to email, you can usehttps://bigfile.bcm.edu/
> ...
>
> meer lezen »
//If build EMAN with libftgl.a
ENABLE_STATIC_FTGL:BOOL=OFF
//enable TAO support
ENABLE_TAO:BOOL=OFF
ok?
For the rest everything was the same except : ENABLE_X86_64, so I
changed into ON
>
> Sorry you're running into issues :^(
>
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
> Sorry you're running into issues :^(
>
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
> Co-Director National Center For Macromolecular Imaging ARE
> Baylor College of Medicine The converse
>
> meer lezen »
Steven Ludtke
Feb 20, 2012, 10:00:53 AM2/20/12
to em...@googlegroups.com
You can run e2speedtest.py to make sure you're getting appropriate results
Sent from my iPhone
Steve Ludtke
Apr 4, 2012, 9:06:44 AM4/4/12
to em...@googlegroups.com
Never heard back on this. Did you solve your problems eventually ?
> >> To unsubscribe from this group, send email to eman2+unsubscribe@googlegroups.com
Wouter Van Putte
Nov 22, 2012, 6:32:08 AM11/22/12
to em...@googlegroups.com
hi, sorry for the "very late" response.
I went to another lab where they often work with your software and there things worked perfectly with the data I had on their computers. I think the main problem was that I loaded to much files at once (i.e. 2000 *.mrc files), which always created an error file. So I had to load them in multiple steps. Another thing that helped was putting the Micrograph folder not in the processing folder, so everythime a bug came I could easily continue by just making a new folder and using the pos/box files. Anyway I am now working with the new version of your software back on my own pc and I don't have any problems anymore. I think this version is really nice to work with...
so many thanks for the help,
Wouter
Op woensdag 4 april 2012 15:06:44 UTC+2 schreef Steve Ludtke het volgende:
I went to another lab where they often work with your software and there things worked perfectly with the data I had on their computers. I think the main problem was that I loaded to much files at once (i.e. 2000 *.mrc files), which always created an error file. So I had to load them in multiple steps. Another thing that helped was putting the Micrograph folder not in the processing folder, so everythime a bug came I could easily continue by just making a new folder and using the pos/box files. Anyway I am now working with the new version of your software back on my own pc and I don't have any problems anymore. I think this version is really nice to work with...
so many thanks for the help,
Wouter
Op woensdag 4 april 2012 15:06:44 UTC+2 schreef Steve Ludtke het volgende:
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