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= BDF failed work with global array. = Filename for all kind of local orbitals in BDF:
{{{
 1. localorb - local orbital generated by BDF module localmo. Boys and trust region methods are used in orbital localization.
 2. blmo - Boys.
 3. tlmo - Trust region.
 4. flmoorb - fragment local orbital generated by bottom-up method.
 5. pflmo - norm-orthogonal pFLMO.
}}}
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When I run BDF with global array support, I encounter such errors, == BDF git version control user's guide ==
Start from a clean BDF copy bdfpkg
{{{
Create directory
  cd bdfpkg
Initial a git bare repository. Notice we also use flag --shared.
  git init --bare --shared
  git add
  git config --global user.name "your name"
  git config --global user.email "youremail@domain"
  git commit -m "Creat BDF package store"
}}}
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0:Segmentation Violation error, status=: 11
(rank:0 hostname:Sodium pid:22041):ARMCI DASSERT fail. src/common/signaltrap.c:SigSegvHandler():310 cond:0
1:Segmentation Violation error, status=: 11
(rank:1 hostname:Sodium pid:22042):ARMCI DASSERT fail. src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 0:: No such file or directory
Last System Error Message from Task 1:: No such file or directory		 == get a bdf work copy ==
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This may be caused by internal BLAS is used when I compile with GA, while I compile BDF program with external BLAS and Lapack library MKL. {{{
Obtain a bdf work copy
  git clone youname@10.105.153.100:/export/gitroot/bdf-pkg
You need set some general information such as user name and user email.
  git config --global user.name "Your name"
  git config --global user.email "youremail@domain"
Create your own branch
  git branch myown
Switch to your new branch
  git checkout myown
}}}

== Some open source Quantum Chemistry program package ==
=== Octopus ===

{{{
    Keywords: Real time TDDFT, Real-space, finite element basis sets, Pseudopotentials
    Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Manual:About_Octopus
    License: GPL
}}}

=== BigDFT ===
{{{
   Keywords: Pseudopotentials, Wavelet basis set,
   Homepage: http://bigdft.org/Wiki/index.php?title=BigDFT_website
   License: GPL
}}}

== Use BDF with job management system ==

=== qsub ===
{{{
You should prepare a qsub script.


}}}

=== bsub ===
{{{
You should prepare a bsub script "my job".

# Set job parameters
#BSUB -a openmpi
#BSUB -J jobname
#BSUB -oo jobname.out
#BSUB -eo jobname.err

# Set number of CPUs
#BSUB -n 6

# get host list
echo /dev/null > nodelist

for host in $LSB_HOSTS ; do
  echo $host >> nodelist
done


# Start BDF MPI job
$BDFHOME/sbin/bdfdrv.py -np nnodes:nprocess:nthreads -machinefile nodelist jobname.inp

}}}

Bingbing Suo is own page.

Wiki logs

1 Add Wiki theme moin-mandarin. Look at the link https://bitbucket.org/thesheep/moin-mandarin

2 Try to edit a bdftheme from modernized theme.

  1. Make a copy of the 'modern' theme in the static files directory and call it 'bdftheme'
  2. Copy the script of this theme MoinMoin/theme/modern.py' to data/plugins/theme/bdftheme.py
  3. Edit the file 'bdftheme.py' and change at least the variable name = "modernized" to {name ="bdftheme"

Filename for all kind of local orbitals in BDF: 

 1. localorb   - local orbital generated by BDF module localmo. Boys and trust region methods are used in orbital localization. 
 2. blmo  - Boys.
 3. tlmo  - Trust region.
 4. flmoorb - fragment local orbital generated by bottom-up method.
 5. pflmo  - norm-orthogonal pFLMO.

BDF git version control user's guide

Start from a clean BDF copy bdfpkg 

Create directory
  cd bdfpkg
Initial a git bare repository. Notice we also use flag --shared. 
  git init --bare --shared
  git add
  git config --global user.name "your name"
  git config --global user.email "youremail@domain"
  git commit -m "Creat BDF package store"

get a bdf work copy

Obtain a bdf work copy
  git clone youname@10.105.153.100:/export/gitroot/bdf-pkg
You need set some general information such as user name and user email.
  git config --global user.name "Your name"
  git config --global user.email "youremail@domain"
Create your own branch
  git branch myown
Switch to your new branch
  git checkout myown

Some open source Quantum Chemistry program package

Octopus

    Keywords: Real time TDDFT, Real-space, finite element basis sets, Pseudopotentials
    Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Manual:About_Octopus
    License: GPL

BigDFT

   Keywords:    Pseudopotentials, Wavelet basis set,
   Homepage:  http://bigdft.org/Wiki/index.php?title=BigDFT_website
   License: GPL

Use BDF with job management system

qsub

You should prepare a qsub script.

bsub

You should prepare a bsub script "my job".

# Set job parameters
#BSUB -a openmpi 
#BSUB -J jobname
#BSUB -oo jobname.out
#BSUB -eo jobname.err

# Set number of CPUs
#BSUB -n 6

# get host list
echo /dev/null > nodelist

for host in $LSB_HOSTS ; do
  echo $host >> nodelist
done


# Start BDF MPI job
$BDFHOME/sbin/bdfdrv.py -np nnodes:nprocess:nthreads -machinefile nodelist jobname.inp

Bingbing Suo (last edited 2023-05-30 14:27:17 by bsuo)