scipion-users — Mailing list for Scipion users

Re: [scipion-users] Eman2.12 error: no such file or directory

[Grigory S. <sha...@gm...>]

Hi Pablo,

I have not tried EMAN2 with mpi in Scipion yet, but my guess is that
scratchdir does not exist..

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
Institute of Genetics and Molecular and Cellular Biology
Integrated Structural Biology Department (CBI)
1, rue Laurent Fries
67404 Illkirch, France
tel. 03 69 48 51 00
e-mail: sh...@ig...

On Thu, Mar 17, 2016 at 2:44 PM, Pablo <p.c...@gm...> wrote:

> Hi! Does anyone know why this might be happening? (Running eman initial
> volume.)
>
> Must say this is a special setup (not the standard Scipion one) but from
> source code, using web-develop branch (but that protocol runs fine in my
> machine, same source code)
>
> Is it some setup problem?
>
>
> Exception in thread Thread-1:
> 00048: Traceback (most recent call last):
> 00049: File
> ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", line
> 551, in __bootstrap_inner
> 00050: self.run()
> 00051: File
> ".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", line
> 504, in run
> 00052: self.__target(*self.__args, **self.__kwargs)
> 00053: File ".../scipion/software/em/eman2.12/lib/EMAN2PAR.py", line 577,
> in run
> 00054:
> proc=subprocess.Popen(["e2parallel.py","localclient","--taskin=%s/%07d"%(self.scratchdir,self.nextid),"--taskout=%s/%07d.out"%(self.scratchdir,self.nextid)])
>
> 00055: File
> ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", line
> 679, in __init__
> 00056: errread, errwrite)
> 00057: File
> ".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", line
> 1249, in execute child
> 00058: raise child_exception
> 00059: OSError: [Errno 2] No such file or directory
>
> (Have replaced actual path in the log with "...", but those paths exists.).
>
>
> All the best, Pablo.
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
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>
>

[scipion-users] Eman2.12 error: no such file or directory

[Pablo <p.c...@gm...>]

Hi! Does anyone know why this might be happening? (Running eman initial 
volume.)

Must say this is a special setup (not the standard Scipion one) but from 
source code, using web-develop branch (but that protocol runs fine in my 
machine, same source code)

Is it some setup problem?


Exception in thread Thread-1:
00048: Traceback (most recent call last):
00049: File 
".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", 
line 551, in __bootstrap_inner
00050: self.run()
00051: File 
".../scipion/software/em/eman2.12/Python/lib/python2.7/threading.py", 
line 504, in run
00052: self.__target(*self.__args, **self.__kwargs)
00053: File ".../scipion/software/em/eman2.12/lib/EMAN2PAR.py", line 
577, in run
00054: 
proc=subprocess.Popen(["e2parallel.py","localclient","--taskin=%s/%07d"%(self.scratchdir,self.nextid),"--taskout=%s/%07d.out"%(self.scratchdir,self.nextid)]) 

00055: File 
".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", 
line 679, in __init__
00056: errread, errwrite)
00057: File 
".../scipion/software/em/eman2.12/Python/lib/python2.7/subprocess.py", 
line 1249, in execute child
00058: raise child_exception
00059: OSError: [Errno 2] No such file or directory

(Have replaced actual path in the log with "...", but those paths exists.).


All the best, Pablo.

Re: [scipion-users] support for a new IMAGIC header format

[Jose M. de la R. T. <del...@gm...>]

Dear Grigory,

Thanks for the feedback, we were not aware of this issue. We will plan to
extend the Xmipp image library to support this.
In the meantime, we could use Eman to write the images in the proper Imagic
format for this protocol.
Even if Eman uses Python, we should write this in a separated script that
run with Eman's Python, to avoid conflict
with Scipion's Python.

Bests,
Jose Miguel.

On Mon, Mar 7, 2016 at 12:16 PM, Grigory Sharov <sha...@gm...>
wrote:

> Dear Scipion developers,
>
> while I was trying to integrate some IMAGIC protocols into Scipion, I have
> discovered that xmipp does not support (rwIMAGIC.cpp
> <https://github.com/I2PC/scipion/blob/master/software/em/xmipp/libraries/data/rwIMAGIC.cpp>)
> new IMAGIC header format (including 3d volumes, stacks of 3d etc; released
> 5 years ago). I was wondering if it is planned to implement such support?
>
> For example, EMAN2 supports both old and new formats but writes img files
> in a new format (see old format
> <https://github.com/cryoem/eman2/blob/master/libEM/imagicio.cpp> and new
> format <https://github.com/cryoem/eman2/blob/master/libEM/imagicio2.cpp>)
>
> The problem is that new IMAGIC cant read files created via xmipp
> ImageHandler class:
>
>  **WARNING: Incorrect floating point type found. The
>>             file was probably not created by IMAGIC.
>>             Floating point type found in file       = 1888088784
>>             Trying to use local floating point type = 33686018
>>             but IMAGIC commands can crash or may go wrong
>>             (READ_DATA_FROM_FILE)
>>
>>
>> Image name, parameters [and history]:
>> Runs/000064_ImagicProtMSA/input_particles.img!@���*�
>> Size: 80, 80  Loc: 1  Type: REAL  Cre.Date: 03-Jul-0116  Time: 12:14:04
>> ��*��p��*��p��*
>> ��p��*����*�����2\��*Ў\��*@����*@�����p�
>> ���p����(7���*0p��p����p�
>>
>>  **WARNING: Incorrect floating point type found. The
>>             file was probably not created by IMAGIC.
>>             Floating point type found in file       = 1888088784
>>             Trying to use local floating point type = 33686018
>>             but IMAGIC commands can crash or may go wrong
>>             (READ_DATA_FROM_FILE)
>>
>>
>>  **ERROR: Inconsistent header values found
>>           Number of all 2D sections = 876
>>           Z dimension (IZLP)        = 16
>>
>>  ***************************************
>>   ERROR in program/subroutine: HEADERS
>>  ***************************************
>
>
>
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
> Institute of Genetics and Molecular and Cellular Biology
> Integrated Structural Biology Department (CBI)
> 1, rue Laurent Fries
> 67404 Illkirch, France
> tel. 03 69 48 51 00
> e-mail: sh...@ig...
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://makebettercode.com/inteldaal-eval
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] support for a new IMAGIC header format

[Grigory S. <sha...@gm...>]

Dear Scipion developers,

while I was trying to integrate some IMAGIC protocols into Scipion, I have
discovered that xmipp does not support (rwIMAGIC.cpp
<https://github.com/I2PC/scipion/blob/master/software/em/xmipp/libraries/data/rwIMAGIC.cpp>)
new IMAGIC header format (including 3d volumes, stacks of 3d etc; released
5 years ago). I was wondering if it is planned to implement such support?

For example, EMAN2 supports both old and new formats but writes img files
in a new format (see old format
<https://github.com/cryoem/eman2/blob/master/libEM/imagicio.cpp> and new
format <https://github.com/cryoem/eman2/blob/master/libEM/imagicio2.cpp>)

The problem is that new IMAGIC cant read files created via xmipp
ImageHandler class:

 **WARNING: Incorrect floating point type found. The
>             file was probably not created by IMAGIC.
>             Floating point type found in file       = 1888088784
>             Trying to use local floating point type = 33686018
>             but IMAGIC commands can crash or may go wrong
>             (READ_DATA_FROM_FILE)
>
>
> Image name, parameters [and history]:
> Runs/000064_ImagicProtMSA/input_particles.img!@���*�
> Size: 80, 80  Loc: 1  Type: REAL  Cre.Date: 03-Jul-0116  Time: 12:14:04
> ��*��p��*��p��*
> ��p��*����*�����2\��*Ў\��*@����*@�����p�
> ���p����(7���*0p��p����p�
>
>  **WARNING: Incorrect floating point type found. The
>             file was probably not created by IMAGIC.
>             Floating point type found in file       = 1888088784
>             Trying to use local floating point type = 33686018
>             but IMAGIC commands can crash or may go wrong
>             (READ_DATA_FROM_FILE)
>
>
>  **ERROR: Inconsistent header values found
>           Number of all 2D sections = 876
>           Z dimension (IZLP)        = 16
>
>  ***************************************
>   ERROR in program/subroutine: HEADERS
>  ***************************************




Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
Institute of Genetics and Molecular and Cellular Biology
Integrated Structural Biology Department (CBI)
1, rue Laurent Fries
67404 Illkirch, France
tel. 03 69 48 51 00
e-mail: sh...@ig...

Re: [scipion-users] Scipion help

[Pablo C. <pc...@cn...>]

Hi Jason.

We still do not support MAC, although we have made some attempts.

Actually, last Friday, we've tried again in order to give you a positive 
answer, with no luck.

We even have a MAC installation page 
<https://github.com/I2PC/scipion/wiki/Installing-on-Mac> sketched with 
our progress but haven't got any success.

So, if you want to explore Scipion, I guess the best option for you, 
since you defined yourself as "very novice", would be to setup a virtual 
machine with ubuntu, and install it there.

It's not optimal, but will allow you to explore our software and 
evaluate it. Is that an option? If so this might be helpful --> 
https://www.youtube.com/watch?v=_42JLz2izBU

Let us know how it goes....

All the best, Pablo.


On 03/03/16 16:14, Jason Pierson wrote:
> I am trying to install Scipion on my Macbook pro but I am very novice 
> at image processing and installing academic packages for personal use 
> so I am having difficulty finalizing the instal. Could you please take 
> a look at the attached image and provide me with any feedback on how 
> to start using Scipion? I have tried to install the package but 
> receive many ‘red’ warnings. How should I fix them in the .conf file? 
> Again, very novice so please bear with me as a beginner.
>
> Thanks,
> Jason
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
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>
>
> _______________________________________________
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> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

[scipion-users] Scipion help

[Jason P. <jlp...@ya...>]

I am trying to install Scipion on my Macbook pro but I am very novice at image processing and installing academic packages for personal use so I am having difficulty finalizing the instal. Could you please take a look at the attached image and provide me with any feedback on how to start using Scipion? I have tried to install the package but receive many ‘red’ warnings. How should I fix them in the .conf file? Again, very novice so please bear with me as a beginner.

Thanks,
Jason

Re: [scipion-users] Relion star files are wrong?

[Jose M. de la R. T. <del...@gm...>]

Dear Grigory,

Thanks for this feedback. Certainly we should check this issue in the
Relion protocols (and others that use the same information).
It would be useful to know if Relion really use the Magnification or
DetectorPixelSize if you give the correct Pixel Size (or SamplingRate) in
Ang/Pixels.

Apart from that, I think you have set wrong parameters in the import.
Ts = Sampling Rate (Ang/Pix)
M = Magnification
D = Detector pixel size

Ts = D / M

In your example, the second numbers are Ok: 140000 / 31818 = 4.4
But your initial parameters to the import are wrong: 140000 / 59000 = 2.37
(and not the 1.1 that you have provide, for this value the detector pixel
size is 6.5 and not 14)

Anyway lets take a look at the protocols and fix this issue.

Kind regards,
Jose Miguel.


On Tue, Feb 16, 2016 at 7:51 PM, Grigory Sharov <sha...@gm...>
wrote:

> Hello!
>
> I have noticed that in scipion-produced relion star files (after 2d
> classification relion protocol) the_rlnMagnification column is wrong (it
> prints nominal 59000 instead of actual 31818) and there is no
> _rlnDetectorPixelSize column in output star files.
>
> That's why I wonder what values should be used for Magnification during
> Micrograph import protocol?
>
> I have used 59000x and 1.1A/px ("from image") during import.
> Classification was done on C4 data, hence pixel size 4.4A. Actual mag
> should be then 4.4/14um=31818 and not 59000 in star file, given our
> detector size 14um.
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
> Institute of Genetics and Molecular and Cellular Biology
> Integrated Structural Biology Department (CBI)
> 1, rue Laurent Fries
> 67404 Illkirch, France
> tel. 03 69 48 51 00
> e-mail: sh...@ig...
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] Question Regarding Image Conversion in Xmipp

[Jagan M. <o....@gm...>]

Dear Jose,
I just checked in xmipp_showj and the two images seem to be right. But when
I open the same in bshow or 3dmod, one seems to be mirrored with respect to
the other. I don't know why.



Regards,
Jagan

On Wed, Feb 17, 2016 at 11:24 AM, Jagan Mohan <o....@gm...> wrote:

> Dear Jose,
>
> Please find attached the jpg file and the spi file which was the output of
> -
>
> xmipp_image_convert -i sample.jpg -o sample.spi --oext spi
>
> Am I missing something?
>
>
> Thanks and Regards,
> Jagan
>
>
> On Wed, Feb 17, 2016 at 11:17 AM, Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Dear Jagan,
>>
>> I tested to convert from .jpg to .spi and both shows the y axis in the
>> same direction.
>> Could you provide us a test .jpg images that reproduce the problem you
>> mention?
>>
>> Bests
>> Jose Miguel.
>>
>> On Wed, Feb 17, 2016 at 11:05 AM, Jagan Mohan <o....@gm...> wrote:
>>
>>> Dear All,
>>>
>>> I am using xmipp_image_convert to convert from a .jpg file to .spi file.
>>> After conversion the output image is mirrored. Is this normal behaviour?
>>> If so, then do I have to then use transform_geometry to generate the
>>> mirror of the output to get my original image back?
>>>
>>>
>>> Regards,
>>> Jagan
>>> --
>>> -{[O]}-
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>
>
>
> --
> -{[O]}-
>



-- 
-{[O]}-

Re: [scipion-users] Question Regarding Image Conversion in Xmipp

[Jagan M. <o....@gm...>]

Dear Jose,

Please find attached the jpg file and the spi file which was the output of -

xmipp_image_convert -i sample.jpg -o sample.spi --oext spi

Am I missing something?


Thanks and Regards,
Jagan


On Wed, Feb 17, 2016 at 11:17 AM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Dear Jagan,
>
> I tested to convert from .jpg to .spi and both shows the y axis in the
> same direction.
> Could you provide us a test .jpg images that reproduce the problem you
> mention?
>
> Bests
> Jose Miguel.
>
> On Wed, Feb 17, 2016 at 11:05 AM, Jagan Mohan <o....@gm...> wrote:
>
>> Dear All,
>>
>> I am using xmipp_image_convert to convert from a .jpg file to .spi file.
>> After conversion the output image is mirrored. Is this normal behaviour?
>> If so, then do I have to then use transform_geometry to generate the
>> mirror of the output to get my original image back?
>>
>>
>> Regards,
>> Jagan
>> --
>> -{[O]}-
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>


-- 
-{[O]}-

Re: [scipion-users] Question Regarding Image Conversion in Xmipp

[Jose M. de la R. T. <del...@gm...>]

Dear Jagan,

I tested to convert from .jpg to .spi and both shows the y axis in the same
direction.
Could you provide us a test .jpg images that reproduce the problem you
mention?

Bests
Jose Miguel.

On Wed, Feb 17, 2016 at 11:05 AM, Jagan Mohan <o....@gm...> wrote:

> Dear All,
>
> I am using xmipp_image_convert to convert from a .jpg file to .spi file.
> After conversion the output image is mirrored. Is this normal behaviour?
> If so, then do I have to then use transform_geometry to generate the
> mirror of the output to get my original image back?
>
>
> Regards,
> Jagan
> --
> -{[O]}-
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] Question Regarding Image Conversion in Xmipp

[Jagan M. <o....@gm...>]

Dear All,

I am using xmipp_image_convert to convert from a .jpg file to .spi file.
After conversion the output image is mirrored. Is this normal behaviour?
If so, then do I have to then use transform_geometry to generate the mirror
of the output to get my original image back?


Regards,
Jagan
-- 
-{[O]}-

[scipion-users] Relion star files are wrong?

[Grigory S. <sha...@gm...>]

Hello!

I have noticed that in scipion-produced relion star files (after 2d
classification relion protocol) the_rlnMagnification column is wrong (it
prints nominal 59000 instead of actual 31818) and there is no
_rlnDetectorPixelSize column in output star files.

That's why I wonder what values should be used for Magnification during
Micrograph import protocol?

I have used 59000x and 1.1A/px ("from image") during import. Classification
was done on C4 data, hence pixel size 4.4A. Actual mag should be then
4.4/14um=31818 and not 59000 in star file, given our detector size 14um.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
Institute of Genetics and Molecular and Cellular Biology
Integrated Structural Biology Department (CBI)
1, rue Laurent Fries
67404 Illkirch, France
tel. 03 69 48 51 00
e-mail: sh...@ig...

Re: [scipion-users] Error while Installing Scipion - LAPACK

[Jagan M. <o....@gm...>]

Yeah I hope so too. I am also trying to figure it out.
This is exactly what I added to get Lapack installed -

set(CMAKE_C_FLAGS "-O3 -DADD_")

in file CMakeLists.txt

On Sat, Feb 13, 2016 at 7:56 PM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Thanks Jagan...let's see if Jesus have any clue with the other problem.
>
> On Sat, Feb 13, 2016 at 7:52 PM, Jagan Mohan <o....@gm...> wrote:
>
>> Dear Jose,
>> I had to set the CFLAGS in CMakeLists.txt file and then run the make and
>> make install. That solved the problem.
>>
>>
>> Regards,
>> Jagan
>>
>> On Sat, Feb 13, 2016 at 7:35 PM, Jose Miguel de la Rosa Trevin <
>> del...@gm...> wrote:
>>
>>> Dear Jagan,
>>>
>>> Can you tell me what you did to get lapack to compile? About the numpy
>>> problem, I haven't seen this issue before. I'm adding Jesus Cuenca (our
>>> system manager) to get some help from him.
>>>
>>> Best
>>> Jose Miguel.
>>>
>>> On Sat, Feb 13, 2016 at 3:38 PM, Jagan Mohan <o....@gm...> wrote:
>>>
>>>> Dear Jose,
>>>> I managed to get past the lapack error. However, I am now stuck at
>>>> numpy. Following is the error I get -
>>>>
>>>> compile options: '-Inumpy/core/src/private -Inumpy/core/src
>>>> -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
>>>> -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include
>>>> -I/gpfs/home/obbineni_j/em_soft/scipion/software/include/python2.7 -c'
>>>> gcc: _configtest.c
>>>> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
>>>> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
>>>> object file: No such file or directory
>>>> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
>>>> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
>>>> object file: No such file or directory
>>>> failure.
>>>>
>>>>
>>>> I have checked my LD_LIBRARY_PATH variable and libcloog-isl.so.4 is in
>>>> it. Do you know why I am getting this error?
>>>>
>>>>
>>>> Thanks and Regards,
>>>> Jagan
>>>>
>>>> On Fri, Feb 12, 2016 at 6:11 PM, Jagan Mohan <o....@gm...> wrote:
>>>>
>>>>> Dear Jose,
>>>>> Thank you for the reply. I will post to the Scipion mailing list in
>>>>> future. I tried the suggestion in the post but still get the same error.
>>>>> Maybe I am doing something wrong.
>>>>> I tried to copy the make.inc.example file to make.inc and added
>>>>> "-DADD_" to the CFLAGS. Is it right?
>>>>>
>>>>>
>>>>> Regards,
>>>>> Jagan
>>>>>
>>>>> On Fri, Feb 12, 2016 at 5:12 PM, Jose Miguel de la Rosa Trevin <
>>>>> del...@gm...> wrote:
>>>>>
>>>>>> Dear Jagan,
>>>>>>
>>>>>> Please use the scipion-users list (in CC), we will move also Xmipp
>>>>>> related question to this one.
>>>>>>
>>>>>> About the problem of installing lapack, I searched in google and
>>>>>> found something that can helps:
>>>>>>
>>>>>> http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=4564
>>>>>>
>>>>>> You can launch the same *cmake* command directly from the lapack
>>>>>> build directory and then continue with the normal scipion installation.
>>>>>>
>>>>>> Hope this helps
>>>>>> Jose Miguel.
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> -{[O]}-
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -{[O]}-
>>>>
>>>
>>>
>>
>>
>> --
>> -{[O]}-
>>
>
>


-- 
-{[O]}-

Re: [scipion-users] Error while Installing Scipion - LAPACK

[Jose M. de la R. T. <del...@gm...>]

Thanks Jagan...let's see if Jesus have any clue with the other problem.

On Sat, Feb 13, 2016 at 7:52 PM, Jagan Mohan <o....@gm...> wrote:

> Dear Jose,
> I had to set the CFLAGS in CMakeLists.txt file and then run the make and
> make install. That solved the problem.
>
>
> Regards,
> Jagan
>
> On Sat, Feb 13, 2016 at 7:35 PM, Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Dear Jagan,
>>
>> Can you tell me what you did to get lapack to compile? About the numpy
>> problem, I haven't seen this issue before. I'm adding Jesus Cuenca (our
>> system manager) to get some help from him.
>>
>> Best
>> Jose Miguel.
>>
>> On Sat, Feb 13, 2016 at 3:38 PM, Jagan Mohan <o....@gm...> wrote:
>>
>>> Dear Jose,
>>> I managed to get past the lapack error. However, I am now stuck at
>>> numpy. Following is the error I get -
>>>
>>> compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
>>> -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
>>> -Inumpy/core/src/npysort -Inumpy/core/include
>>> -I/gpfs/home/obbineni_j/em_soft/scipion/software/include/python2.7 -c'
>>> gcc: _configtest.c
>>> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
>>> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
>>> object file: No such file or directory
>>> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
>>> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
>>> object file: No such file or directory
>>> failure.
>>>
>>>
>>> I have checked my LD_LIBRARY_PATH variable and libcloog-isl.so.4 is in
>>> it. Do you know why I am getting this error?
>>>
>>>
>>> Thanks and Regards,
>>> Jagan
>>>
>>> On Fri, Feb 12, 2016 at 6:11 PM, Jagan Mohan <o....@gm...> wrote:
>>>
>>>> Dear Jose,
>>>> Thank you for the reply. I will post to the Scipion mailing list in
>>>> future. I tried the suggestion in the post but still get the same error.
>>>> Maybe I am doing something wrong.
>>>> I tried to copy the make.inc.example file to make.inc and added
>>>> "-DADD_" to the CFLAGS. Is it right?
>>>>
>>>>
>>>> Regards,
>>>> Jagan
>>>>
>>>> On Fri, Feb 12, 2016 at 5:12 PM, Jose Miguel de la Rosa Trevin <
>>>> del...@gm...> wrote:
>>>>
>>>>> Dear Jagan,
>>>>>
>>>>> Please use the scipion-users list (in CC), we will move also Xmipp
>>>>> related question to this one.
>>>>>
>>>>> About the problem of installing lapack, I searched in google and found
>>>>> something that can helps:
>>>>>
>>>>> http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=4564
>>>>>
>>>>> You can launch the same *cmake* command directly from the lapack
>>>>> build directory and then continue with the normal scipion installation.
>>>>>
>>>>> Hope this helps
>>>>> Jose Miguel.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -{[O]}-
>>>>
>>>
>>>
>>>
>>> --
>>> -{[O]}-
>>>
>>
>>
>
>
> --
> -{[O]}-
>

Re: [scipion-users] Error while Installing Scipion - LAPACK

[Jagan M. <o....@gm...>]

Dear Jose,
I had to set the CFLAGS in CMakeLists.txt file and then run the make and
make install. That solved the problem.


Regards,
Jagan

On Sat, Feb 13, 2016 at 7:35 PM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Dear Jagan,
>
> Can you tell me what you did to get lapack to compile? About the numpy
> problem, I haven't seen this issue before. I'm adding Jesus Cuenca (our
> system manager) to get some help from him.
>
> Best
> Jose Miguel.
>
> On Sat, Feb 13, 2016 at 3:38 PM, Jagan Mohan <o....@gm...> wrote:
>
>> Dear Jose,
>> I managed to get past the lapack error. However, I am now stuck at numpy.
>> Following is the error I get -
>>
>> compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
>> -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
>> -Inumpy/core/src/npysort -Inumpy/core/include
>> -I/gpfs/home/obbineni_j/em_soft/scipion/software/include/python2.7 -c'
>> gcc: _configtest.c
>> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
>> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
>> object file: No such file or directory
>> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
>> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
>> object file: No such file or directory
>> failure.
>>
>>
>> I have checked my LD_LIBRARY_PATH variable and libcloog-isl.so.4 is in
>> it. Do you know why I am getting this error?
>>
>>
>> Thanks and Regards,
>> Jagan
>>
>> On Fri, Feb 12, 2016 at 6:11 PM, Jagan Mohan <o....@gm...> wrote:
>>
>>> Dear Jose,
>>> Thank you for the reply. I will post to the Scipion mailing list in
>>> future. I tried the suggestion in the post but still get the same error.
>>> Maybe I am doing something wrong.
>>> I tried to copy the make.inc.example file to make.inc and added "-DADD_"
>>> to the CFLAGS. Is it right?
>>>
>>>
>>> Regards,
>>> Jagan
>>>
>>> On Fri, Feb 12, 2016 at 5:12 PM, Jose Miguel de la Rosa Trevin <
>>> del...@gm...> wrote:
>>>
>>>> Dear Jagan,
>>>>
>>>> Please use the scipion-users list (in CC), we will move also Xmipp
>>>> related question to this one.
>>>>
>>>> About the problem of installing lapack, I searched in google and found
>>>> something that can helps:
>>>>
>>>> http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=4564
>>>>
>>>> You can launch the same *cmake* command directly from the lapack build
>>>> directory and then continue with the normal scipion installation.
>>>>
>>>> Hope this helps
>>>> Jose Miguel.
>>>>
>>>
>>>
>>>
>>> --
>>> -{[O]}-
>>>
>>
>>
>>
>> --
>> -{[O]}-
>>
>
>


-- 
-{[O]}-

Re: [scipion-users] Error while Installing Scipion - LAPACK

[Jose M. de la R. T. <del...@gm...>]

Dear Jagan,

Can you tell me what you did to get lapack to compile? About the numpy
problem, I haven't seen this issue before. I'm adding Jesus Cuenca (our
system manager) to get some help from him.

Best
Jose Miguel.

On Sat, Feb 13, 2016 at 3:38 PM, Jagan Mohan <o....@gm...> wrote:

> Dear Jose,
> I managed to get past the lapack error. However, I am now stuck at numpy.
> Following is the error I get -
>
> compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
> -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
> -Inumpy/core/src/npysort -Inumpy/core/include
> -I/gpfs/home/obbineni_j/em_soft/scipion/software/include/python2.7 -c'
> gcc: _configtest.c
> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
> object file: No such file or directory
> /gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
> error while loading shared libraries: libcloog-isl.so.4: cannot open shared
> object file: No such file or directory
> failure.
>
>
> I have checked my LD_LIBRARY_PATH variable and libcloog-isl.so.4 is in it.
> Do you know why I am getting this error?
>
>
> Thanks and Regards,
> Jagan
>
> On Fri, Feb 12, 2016 at 6:11 PM, Jagan Mohan <o....@gm...> wrote:
>
>> Dear Jose,
>> Thank you for the reply. I will post to the Scipion mailing list in
>> future. I tried the suggestion in the post but still get the same error.
>> Maybe I am doing something wrong.
>> I tried to copy the make.inc.example file to make.inc and added "-DADD_"
>> to the CFLAGS. Is it right?
>>
>>
>> Regards,
>> Jagan
>>
>> On Fri, Feb 12, 2016 at 5:12 PM, Jose Miguel de la Rosa Trevin <
>> del...@gm...> wrote:
>>
>>> Dear Jagan,
>>>
>>> Please use the scipion-users list (in CC), we will move also Xmipp
>>> related question to this one.
>>>
>>> About the problem of installing lapack, I searched in google and found
>>> something that can helps:
>>>
>>> http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=4564
>>>
>>> You can launch the same *cmake* command directly from the lapack build
>>> directory and then continue with the normal scipion installation.
>>>
>>> Hope this helps
>>> Jose Miguel.
>>>
>>
>>
>>
>> --
>> -{[O]}-
>>
>
>
>
> --
> -{[O]}-
>

Re: [scipion-users] Error while Installing Scipion - LAPACK

[Jagan M. <o....@gm...>]

Dear Jose,
I managed to get past the lapack error. However, I am now stuck at numpy.
Following is the error I get -

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
-Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
-Inumpy/core/src/npysort -Inumpy/core/include
-I/gpfs/home/obbineni_j/em_soft/scipion/software/include/python2.7 -c'
gcc: _configtest.c
/gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
error while loading shared libraries: libcloog-isl.so.4: cannot open shared
object file: No such file or directory
/gpfs/home/sys/opt/gcc/gcc-4.7.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/cc1:
error while loading shared libraries: libcloog-isl.so.4: cannot open shared
object file: No such file or directory
failure.


I have checked my LD_LIBRARY_PATH variable and libcloog-isl.so.4 is in it.
Do you know why I am getting this error?


Thanks and Regards,
Jagan

On Fri, Feb 12, 2016 at 6:11 PM, Jagan Mohan <o....@gm...> wrote:

> Dear Jose,
> Thank you for the reply. I will post to the Scipion mailing list in
> future. I tried the suggestion in the post but still get the same error.
> Maybe I am doing something wrong.
> I tried to copy the make.inc.example file to make.inc and added "-DADD_"
> to the CFLAGS. Is it right?
>
>
> Regards,
> Jagan
>
> On Fri, Feb 12, 2016 at 5:12 PM, Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Dear Jagan,
>>
>> Please use the scipion-users list (in CC), we will move also Xmipp
>> related question to this one.
>>
>> About the problem of installing lapack, I searched in google and found
>> something that can helps:
>>
>> http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=4564
>>
>> You can launch the same *cmake* command directly from the lapack build
>> directory and then continue with the normal scipion installation.
>>
>> Hope this helps
>> Jose Miguel.
>>
>
>
>
> --
> -{[O]}-
>



-- 
-{[O]}-

Re: [scipion-users] Error while Installing Scipion - LAPACK

[Jagan M. <o....@gm...>]

Dear Jose,
Thank you for the reply. I will post to the Scipion mailing list in future.
I tried the suggestion in the post but still get the same error. Maybe I am
doing something wrong.
I tried to copy the make.inc.example file to make.inc and added "-DADD_" to
the CFLAGS. Is it right?


Regards,
Jagan

On Fri, Feb 12, 2016 at 5:12 PM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Dear Jagan,
>
> Please use the scipion-users list (in CC), we will move also Xmipp related
> question to this one.
>
> About the problem of installing lapack, I searched in google and found
> something that can helps:
>
> http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=4564
>
> You can launch the same *cmake* command directly from the lapack build
> directory and then continue with the normal scipion installation.
>
> Hope this helps
> Jose Miguel.
>



-- 
-{[O]}-

[scipion-users] Error while Installing Scipion - LAPACK

[Jose M. de la R. T. <del...@gm...>]

Dear Jagan,

Please use the scipion-users list (in CC), we will move also Xmipp related
question to this one.

About the problem of installing lapack, I searched in google and found
something that can helps:

http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=4564

You can launch the same *cmake* command directly from the lapack build
directory and then continue with the normal scipion installation.

Hope this helps
Jose Miguel.

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[Pablo C. <pc...@cn...>]

[scipion-users] Testing

[Pablo C. <pc...@cn...>]