scipion-users

[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] 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.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

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

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

Thanks, Grigory.

Here a colleague told me that eman must run using Threads (it fails with 
MPI).

On 17/03/16 15:12, Grigory Sharov wrote:
> 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... <mailto:sh...@ig...>
>
> On Thu, Mar 17, 2016 at 2:44 PM, Pablo <p.c...@gm... 
> <mailto: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.
>     http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>     _______________________________________________
>     scipion-users mailing list
>     sci...@li...
>     <mailto:sci...@li...>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

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

[Wolfgang L. <w.l...@uk...>]

hi,

the default scipion 1.0 installation mixes up the mpi4py installation 
(in our case).

so first you must put the mpicc etc. in your path and then
extract (from the original homepage) mpi4py-1.3.1.tar.gz
an reinstall the package with the scipion python executable.

then mpi will work.

cheers,
wolfgang



On 03/18/2016 11:21 AM, Pablo Conesa wrote:
> Thanks, Grigory.
>
> Here a colleague told me that eman must run using Threads (it fails 
> with MPI).
>
> On 17/03/16 15:12, Grigory Sharov wrote:
>> 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... 
>> <mailto: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.
>>     http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>>     _______________________________________________
>>     scipion-users mailing list
>>     sci...@li...
>>     <mailto:sci...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users


-- 
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Institute of Molecular Biotechnology (IMBA)
Dr. Bohr-Gasse 3-7 (Room 6.14)
1030 Vienna, Austria
Tel.: +43 (1) 790 44-4649
Email: w.l...@uk...
http://www.cssb-hamburg.de/

--

_____________________________________________________________________

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de
Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
_____________________________________________________________________

SAVE PAPER - THINK BEFORE PRINTING

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

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

Hi Wolfgang,

Thanks for your feedback. There was a bug where the LD_LIBRARY_PATH was
overwritten
for all Python modules that we think is related to the problem you mention.
It was fixed here:
https://github.com/I2PC/scipion/pull/364/files

We should release that in the next bug-fix release (v1.0.1).

Bests,
Jose Miguel.

On Fri, Mar 18, 2016 at 12:14 PM, Wolfgang Lugmayr <w.l...@uk...> wrote:

> hi,
>
> the default scipion 1.0 installation mixes up the mpi4py installation (in
> our case).
>
> so first you must put the mpicc etc. in your path and then
> extract (from the original homepage) mpi4py-1.3.1.tar.gz
> an reinstall the package with the scipion python executable.
>
> then mpi will work.
>
> cheers,
> wolfgang
>
>
>
>
> On 03/18/2016 11:21 AM, Pablo Conesa wrote:
>
> Thanks, Grigory.
>
> Here a colleague told me that eman must run using Threads (it fails with
> MPI).
>
> On 17/03/16 15:12, Grigory Sharov wrote:
>
> 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.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> --
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Institute of Molecular Biotechnology (IMBA)
> Dr. Bohr-Gasse 3-7 (Room 6.14)
> 1030 Vienna, Austria
> Tel.: +43 (1) 790 44-4649
> Email: w.l...@uk...http://www.cssb-hamburg.de/
>
>
> ------------------------------
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen
> Rechts; Gerichtsstand: Hamburg | www.uke.de
> Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr.
> Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
> ------------------------------
>
> SAVE PAPER - THINK BEFORE PRINTING
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>