Re: [votca] Votca-csg Installation Error

[nabil . s . ramlawi]

On Sunday, April 1, 2018 at 11:02:04 AM UTC-5, Christoph Junghans wrote:
>
>
>
> On Sun, Apr 1, 2018, 17:09  wrote:
>
>>
>>
>> On Sunday, April 1, 2018 at 9:57:21 AM UTC-5, Christoph Junghans wrote:
>>>
>>>
>>> On Sun, Apr 1, 2018 at 16:23  wrote:
>>>
 Hello, 
 I am trying to install Votca using build.sh on Stampede 2 cluster which 
 runs on CENTOS. I am loading the required dependencies, but I am getting 
 an 
 error related to the boost libraries:
 "
 /opt/apps/intel17/boost/1.64/include/boost/numeric/ublas/storage.hpp:299:18:
  
 error: ‘make_array’ is not a member of ‘boost::serialization’
  ar & serialization::make_array(data_, s);
 "
 Is it an incompatible boost version? or there is something I am 
 missing? 

>>>
>>> Can you try to build without MKL?
>>>
>>  
>> If I unload MKL from the environment, boost, fftw3 and gsl will be 
>> deactivated. I can ask the admins if there is a way around this. But if 
>> there is not, is there a way to manually deactivating mkl? I just tried 
>> -DWITH_MKL=NO, but this did not change the error.
>>
>
> Try -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON 
>
> This still gave the same error, but with a slightly different error 
message. I attached the log. 

Thanks.

 

> Christoph
>
>>
>> Thanks,
>> Nabil
>>
>>>
>>> Christoph 
>>>

 I attached the error log for more details. 

 Thanks in advance, 
 Nabil

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>>> -- 
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>>>
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>>
>

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This is VOTCA build.sh, version 2.1.7
Install prefix is '/home1/05073/nramlawi/Programs/VOTCA'
Using 29 jobs for make/ninja
Working on tools
Source dir (tools) is already there - skipping checkout
cmake -DCMAKE_INSTALL_PREFIX='/home1/05073/nramlawi/Programs/VOTCA' 
-DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON 
/home1/05073/nramlawi/Programs/VOTCA/src/tools
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /bin/cc
-- Check for working C compiler: /bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /bin/c++
-- Check for working CXX compiler: /bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /opt/apps/git/2.9.0/bin/git (found version "2.9.0") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.64.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1") 
-- Checking for module 'gsl'
--   Found gsl, version 2.3
-- Found GSL: /opt/apps/intel17/gsl/2.3/lib/libgsl.so  
-- Looking for gsl_linalg_QR_decomp in /opt/apps/intel17/gsl/2.3/lib/libgsl.so;
-- Looking for gsl_linalg_QR_decomp in /opt/apps/intel17/gsl/2.3/lib/libgsl.so; 
- not found
-- Found GSLCBLAS: /opt/apps/intel17/gsl/2.3/lib/libgslcblas.so  
-- Looking for cblas_dsyrk in /opt/apps/intel17/gsl/2.3/lib/libgslcblas.so;
-- Looking for cblas_dsyrk in /opt/apps/intel17/gsl/2.3/lib/libgslcblas.so; - 
found
-- Looking for gsl_linalg_QR_lssolve in 

Re: [votca] Votca-csg Installation Error

[nabil . s . ramlawi]

On Sunday, April 1, 2018 at 9:57:21 AM UTC-5, Christoph Junghans wrote:
>
>
> On Sun, Apr 1, 2018 at 16:23  wrote:
>
>> Hello, 
>> I am trying to install Votca using build.sh on Stampede 2 cluster which 
>> runs on CENTOS. I am loading the required dependencies, but I am getting an 
>> error related to the boost libraries:
>> "
>> /opt/apps/intel17/boost/1.64/include/boost/numeric/ublas/storage.hpp:299:18: 
>> error: ‘make_array’ is not a member of ‘boost::serialization’
>>  ar & serialization::make_array(data_, s);
>> "
>> Is it an incompatible boost version? or there is something I am missing? 
>>
>
> Can you try to build without MKL?
>
 
If I unload MKL from the environment, boost, fftw3 and gsl will be 
deactivated. I can ask the admins if there is a way around this. But if 
there is not, is there a way to manually deactivating mkl? I just tried 
-DWITH_MKL=NO, but this did not change the error.

Thanks,
Nabil

>
> Christoph 
>
>>
>> I attached the error log for more details. 
>>
>> Thanks in advance, 
>> Nabil
>>
>> -- 
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>>
> -- 
> Christoph Junghans
> Web: http://www.compphys.de
>

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[votca] Votca-csg Installation Error

[nabil . s . ramlawi]

Hello, 
I am trying to install Votca using build.sh on Stampede 2 cluster which 
runs on CENTOS. I am loading the required dependencies, but I am getting an 
error related to the boost libraries:
"
/opt/apps/intel17/boost/1.64/include/boost/numeric/ublas/storage.hpp:299:18: 
error: ‘make_array’ is not a member of ‘boost::serialization’
 ar & serialization::make_array(data_, s);
"
Is it an incompatible boost version? or there is something I am missing? 
I attached the error log for more details. 

Thanks in advance, 
Nabil

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This is VOTCA build.sh, version 2.1.7
Install prefix is '/home1/05073/nramlawi/Programs/VOTCA'
Using 29 jobs for make/ninja
Working on tools
Source dir (tools) is already there - skipping checkout
cmake -DCMAKE_INSTALL_PREFIX='/home1/05073/nramlawi/Programs/VOTCA'  
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON 
/home1/05073/nramlawi/Programs/VOTCA/src/tools
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /bin/cc
-- Check for working C compiler: /bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /bin/c++
-- Check for working CXX compiler: /bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /opt/apps/git/2.9.0/bin/git (found version "2.9.0") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.64.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1") 
-- Checking for module 'gsl'
--   Found gsl, version 2.3
-- Found GSL: /opt/apps/intel17/gsl/2.3/lib/libgsl.so  
-- Looking for gsl_linalg_QR_decomp in /opt/apps/intel17/gsl/2.3/lib/libgsl.so;
-- Looking for gsl_linalg_QR_decomp in /opt/apps/intel17/gsl/2.3/lib/libgsl.so; 
- not found
-- Found GSLCBLAS: /opt/apps/intel17/gsl/2.3/lib/libgslcblas.so  
-- Looking for cblas_dsyrk in /opt/apps/intel17/gsl/2.3/lib/libgslcblas.so;
-- Looking for cblas_dsyrk in /opt/apps/intel17/gsl/2.3/lib/libgslcblas.so; - 
found
-- Looking for gsl_linalg_QR_lssolve in 
/opt/apps/intel17/gsl/2.3/lib/libgsl.so;/opt/apps/intel17/gsl/2.3/lib/libgslcblas.so;
-- Looking for gsl_linalg_QR_lssolve in 
/opt/apps/intel17/gsl/2.3/lib/libgsl.so;/opt/apps/intel17/gsl/2.3/lib/libgslcblas.so;
 - found
-- Intel(R) MKL was found:
  MKL_INCLUDE_DIRS: 
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include
  MKL_LIBRARY_DIRS: 
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64;/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64
  MKL_LIBRARIES: 
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libmkl_rt.so;/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libiomp5.so;/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libimf.so
-- MKL found, overloading uBLAS prod()
-- Checking for module 'fftw3'
--   Found fftw3, version 3.3.6-pl2
-- Found FFTW3: /opt/apps/intel17/impi17_0/fftw3/3.3.6/lib/libfftw3.so  
-- Looking for fftw_plan_r2r_1d in 
/opt/apps/intel17/impi17_0/fftw3/3.3.6/lib/libfftw3.so;
-- Looking for fftw_plan_r2r_1d in 
/opt/apps/intel17/impi17_0/fftw3/3.3.6/lib/libfftw3.so; - found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map 

Re: [votca] Using Cubic Spline function in Simplex

[nabil . s . ramlawi]

On Friday, January 26, 2018 at 7:59:52 AM UTC-6, Christoph Junghans wrote:
>
> On Thu, Jan 25, 2018 at 9:16 PM,   
> wrote: 
> > Hi, 
> > 
> > I have an application where I need to use the cbspl function with the 
> > simplex optimizer. 
> > Is there a simple way to achieve that? 
> Basically you will have to modify table_functional.sh to turn your 
> cbspl parameters into a table. 
>
> Isn't there a way to utilize the implementation of cbspl already used with 
relative entropy? 
Thanks, 
Nabil 

> Christoph 
> > 
> > Many thanks, 
> > Nabil 
> > 
> > -- 
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>
>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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[votca] Using Cubic Spline function in Simplex

[nabil . s . ramlawi]

Hi, 

I have an application where I need to use the cbspl function with the 
simplex optimizer. 
Is there a simple way to achieve that?

Many thanks, 
Nabil

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Re: [votca] csg_call with convert_potential

[nabil . s . ramlawi]

On Friday, November 3, 2017 at 4:08:58 PM UTC-5, Christoph Junghans wrote:
>
> 2017-11-03 11:35 GMT-06:00  : 
> > 
> > 
> > On Friday, November 3, 2017 at 7:49:29 AM UTC-5, Christoph Junghans 
> wrote: 
> >> 
> >> 
> >> 
> >> On Nov 2, 2017 8:32 PM,  wrote: 
> >> 
> >> Hello, 
> >> 
> >> I am trying to use csg_call to convert the potentials in a certain step 
> to 
> >> lammps format. This is causing an infinite loop in the terminal I issue 
> the 
> >> command in. 
> >> This is the command: csg_call --options settings.xml  --ia-type 
> non-bonded 
> >> --ia-name C-CG convert_potential lammps  --clean C-CG.pot.cur 
> >> C-CG.table.votca.xvg 
> >> 
> >> Can you attach your two input files? 
> >> 
> >> Christoph 
> > 
> > Yes sure.Please find them attached. 
> $ csg_call --options settings.xml  --ia-type non-bonded --ia-name C-CG 
> convert_potential lammps  --clean C-CG.pot.cur C-CG.table.votca.xvg 
> Works perfectly for me with ae71293febcbd4f03bd64b576a2933c46b007f83! 
> Did you modify VOTCA or what version are you using? 
>
> But one thing is strange, your settings.xml  should say: 
> gromacs 
> if you want to convert to lammps, it should be: 
> lammps 
>
> Christoph 
>
 
Thanks Christoph. I modified one script in VOTCA, but it  is not related to 
potential computation. I updated my votca version to the most recent one. 
This fixed the infinite loop issue. 
On the other hand I changed the program to lammps to convert the potential 
and it worked! I originally had gromacs there because I do the optimization 
using gromacs, but then use Lammps to run a different simulation using the 
final potentials. 

Best, 
Nabil 

> >> 
> >> I tried an older version of votca and it did not have this problem 
> >> although I issued the same command. 
> >> What can be the problem? 
> >> Thanks, 
> >> Nabil 
> >> 
> >> -- 
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> >> 
> >> 
> > -- 
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>
>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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Re: [votca] csg_call with convert_potential

[nabil . s . ramlawi]

On Friday, November 3, 2017 at 7:49:29 AM UTC-5, Christoph Junghans wrote:
>
>
>
> On Nov 2, 2017 8:32 PM,  wrote:
>
> Hello, 
>
> I am trying to use csg_call to convert the potentials in a certain step to 
> lammps format. This is causing an infinite loop in the terminal I issue the 
> command in. 
> This is the command: csg_call --options settings.xml  --ia-type non-bonded 
> --ia-name C-CG convert_potential lammps  --clean C-CG.pot.cur 
> C-CG.table.votca.xvg
>
> Can you attach your two input files?
>
> Christoph
>
Yes sure.Please find them attached. 

>
> I tried an older version of votca and it did not have this problem 
> although I issued the same command.
> What can be the problem?
> Thanks,
> Nabil
>
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>
>
>

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settings.xml
Description: XML document


C-CG.pot.cur
Description: Binary data

Re: [votca] Simplex State not Updating

[nabil . s . ramlawi]

Thanks!

Nabil

On Monday, September 25, 2017 at 11:52:59 AM UTC-5, Christoph Junghans 
wrote:
>
> 2017-09-25 9:48 GMT-06:00  : 
> > Hello all, 
> > 
> > I want to use simplex optimizer. I started by trying to run the tutorial 
> > file as a start. Nevertheless while running that example, the simplex 
> state 
> > is not updating after step 7 because the downhill processor script is 
> giving 
> > an error. From skimming through the inverse.log file, my guess is that 
> the 
> > function get_convergence_value defined in CsgSimplex is failing to give 
> the 
> > convergence value. 
> > I tried to change the initial parameter set in CG-CG.simplex.in but it 
> still 
> > did not work. 
> Fixed: 
> https://github.com/votca/csg/commit/ae71293febcbd4f03bd64b576a2933c46b007f83 
>
> Christoph 
> > 
> > Your feedback is appreciated. 
> > 
> > Thanks, 
> > Nabil 
> > 
> > -- 
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> > For more options, visit https://groups.google.com/d/optout. 
>
>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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[votca] Simplex State not Updating

[nabil . s . ramlawi]

Hello all,

I want to use simplex optimizer. I started by trying to run the tutorial 
file as a start. Nevertheless while running that example, the simplex state 
is not updating after step 7 because the downhill processor script is 
giving an error. From skimming through the inverse.log file, my guess is 
that the function get_convergence_value defined in CsgSimplex is failing to 
give the convergence value. 
I tried to change the initial parameter set in CG-CG.simplex.in but it 
still did not work. 

Your feedback is appreciated. 

Thanks, 
Nabil 

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