DISI - User contributions [en]

Conda environment issue

2020-10-29T02:20:52Z

Chinzo: Created page with "'''Simple steps to solve “Segmentation Fault (core dumped)” or “CondaEnvException: Pip Failed”''' If you get the above error messages during your condo environment cr..."

'''Simple steps to solve “Segmentation Fault (core dumped)” or “CondaEnvException: Pip Failed”'''

If you get the above error messages during your condo environment creation process with .yml file, you need to check if there are packages that incompatible with other packages or current condo environment.

1. In order to find that package that making the error messages you need to split into smaller chunks and install one by one. If you got the same error in your chosen chunk of packages, you need to split into smaller chunks again until you find the bad packages (like a binary search).

2. Another approach is to delete basic package versions. If you want to install a specific version of packages, keep their versions and delete other packages versions from the yml file. For example, You may need exact version of RDKit, Openeye. Keep their package version. And then create the environment with your yml file. That will avoid installing incompatible or all version of packages.

Tin jji

2020-04-06T22:27:03Z

Chinzo: /* Install TIN */

== load tin ==
<pre>
su - xyz
bash
cd /nfs/ex9/work/xyz/tin01
source /mnt/nfs/home/devtest/anaconda3/bin/activate
conda activate /nfs/soft/www/apps/tin01/envs/development
source /nfs/soft/mitools/env.sh
export TIN_HOST="n-5-35"
You can also change the port (default port is 5432)
export TIN_PORT="5432"
zincload-catalog.sh --name mce --skip-depletion H28P03.00.smi
</pre>

== Install TIN ==

First you need to be a root 

<pre>sudo -i</pre>

# Please replace the code with square brackets []

'''1. Python 3.6.7 installation script'''

<pre>/nfs/home/chinzo/code/installation-utilities/install-python36.sh</pre>

'''2. PostgreSQL12 installation script'''
# Please replace /local2. This is your postgres data directory
# In this case script will create a data directory in this directory. For example: '''/local2'''/psql/12/data

<pre>sh /nfs/home/chinzo/code/installation-utilities/install-postgres12.sh [/local2]</pre>

'''3. RDKIT cartridge installation'''

# You need to specify rdkit and python directory.
# /opt/rdkit is directory that you are willing to install rdkit
# /opt/python/3.6.7 is directory that you have already installed it

<pre>/nfs/home/chinzo/code/installation-utilities/install-rdkit.sh [/opt/rdkit] [/opt/python/3.6.7]</pre>

'''4. PostgreSQL12 configuration for TIN'''
<pre>sh /nfs/home/chinzo/code/installation-utilities/postgres-config.sh</pre>

[[Category:Internal]]

Tin jji

2020-04-06T22:26:13Z

Chinzo: /* Install TIN */

== load tin ==
<pre>
su - xyz
bash
cd /nfs/ex9/work/xyz/tin01
source /mnt/nfs/home/devtest/anaconda3/bin/activate
conda activate /nfs/soft/www/apps/tin01/envs/development
source /nfs/soft/mitools/env.sh
export TIN_HOST="n-5-35"
You can also change the port (default port is 5432)
export TIN_PORT="5432"
zincload-catalog.sh --name mce --skip-depletion H28P03.00.smi
</pre>

== Install TIN ==

First you need to be a root 

<pre>sudo - i</pre>

# Please replace the code with square brackets []

'''1. Python 3.6.7 installation script'''

<pre>/nfs/home/chinzo/code/installation-utilities/install-python36.sh</pre>

'''2. PostgreSQL12 installation script'''
# Please replace /local2. This is your postgres data directory
# In this case script will create a data directory in this directory. For example: '''/local2'''/psql/12/data

<pre>sh /nfs/home/chinzo/code/installation-utilities/install-postgres12.sh [/local2]</pre>

'''3. RDKIT cartridge installation'''

# You need to specify rdkit and python directory.
# /opt/rdkit is directory that you are willing to install rdkit
# /opt/python/3.6.7 is directory that you have already installed it

<pre>/nfs/home/chinzo/code/installation-utilities/install-rdkit.sh [/opt/rdkit] [/opt/python/3.6.7]</pre>

'''4. PostgreSQL12 configuration for TIN'''
<pre>sh /nfs/home/chinzo/code/installation-utilities/postgres-config.sh</pre>

[[Category:Internal]]

Tin jji

2020-04-06T22:25:45Z

Chinzo: /* Install TIN */

== load tin ==
<pre>
su - xyz
bash
cd /nfs/ex9/work/xyz/tin01
source /mnt/nfs/home/devtest/anaconda3/bin/activate
conda activate /nfs/soft/www/apps/tin01/envs/development
source /nfs/soft/mitools/env.sh
export TIN_HOST="n-5-35"
You can also change the port (default port is 5432)
export TIN_PORT="5432"
zincload-catalog.sh --name mce --skip-depletion H28P03.00.smi
</pre>

== Install TIN ==

First you need to be a root 

<pre>sudo - i</pre>

# Please replace the code with square brackets []

'''1. Python 3.6.7 installation script'''

<pre>/nfs/home/chinzo/code/installation-utilities/install-python36.sh</pre>

'''2. PostgreSQL12 installation script'''
# Please replace /local2. This is your postgres data directory
# In this case script will create a data directory in this directory
# For example: /local2/psql/12/data

<pre>sh /nfs/home/chinzo/code/installation-utilities/install-postgres12.sh [/local2]</pre>

'''3. RDKIT cartridge installation'''

# You need to specify rdkit and python directory.
# /opt/rdkit is directory that you are willing to install rdkit
# /opt/python/3.6.7 is directory that you have already installed it

<pre>/nfs/home/chinzo/code/installation-utilities/install-rdkit.sh [/opt/rdkit] [/opt/python/3.6.7]</pre>

'''4. PostgreSQL12 configuration for TIN'''
<pre>sh /nfs/home/chinzo/code/installation-utilities/postgres-config.sh</pre>

[[Category:Internal]]

Tin jji

2020-04-06T22:24:57Z

Chinzo: /* install tin */

== load tin ==
<pre>
su - xyz
bash
cd /nfs/ex9/work/xyz/tin01
source /mnt/nfs/home/devtest/anaconda3/bin/activate
conda activate /nfs/soft/www/apps/tin01/envs/development
source /nfs/soft/mitools/env.sh
export TIN_HOST="n-5-35"
You can also change the port (default port is 5432)
export TIN_PORT="5432"
zincload-catalog.sh --name mce --skip-depletion H28P03.00.smi
</pre>

== Install TIN ==

First you need to be a root 

<pre>sudo - i</pre>

# Please replace the code with square brackets []

'''1. Python 3.6.7 installation script'''

<pre>/nfs/home/chinzo/code/installation-utilities/install-python36.sh</pre>

'''2. PostgreSQL12 installation script'''
# Please replace /local2. This is your postgres data directory. In this case 
# Script will create a data directory in this directory
# For example: /local2/psql/12/data

<pre>sh /nfs/home/chinzo/code/installation-utilities/install-postgres12.sh [/local2]</pre>

'''3. RDKIT cartridge installation'''

# You need to specify rdkit and python directory.
# /opt/rdkit is directory that you are willing to install rdkit
# /opt/python/3.6.7 is directory that you have already installed it

<pre>/nfs/home/chinzo/code/installation-utilities/install-rdkit.sh [/opt/rdkit] [/opt/python/3.6.7]</pre>

'''4. PostgreSQL12 configuration for TIN'''
<pre>sh /nfs/home/chinzo/code/installation-utilities/postgres-config.sh</pre>

[[Category:Internal]]

Tin jji

2020-04-06T22:24:35Z

Chinzo: /* install tin */

== load tin ==
<pre>
su - xyz
bash
cd /nfs/ex9/work/xyz/tin01
source /mnt/nfs/home/devtest/anaconda3/bin/activate
conda activate /nfs/soft/www/apps/tin01/envs/development
source /nfs/soft/mitools/env.sh
export TIN_HOST="n-5-35"
You can also change the port (default port is 5432)
export TIN_PORT="5432"
zincload-catalog.sh --name mce --skip-depletion H28P03.00.smi
</pre>

== install tin ==

First you need to be a root 

<pre>sudo - i</pre>

# Please replace the code with square brackets []

'''1. Python 3.6.7 installation script'''

<pre>/nfs/home/chinzo/code/installation-utilities/install-python36.sh</pre>

'''2. PostgreSQL12 installation script'''
# Please replace /local2. This is your postgres data directory. In this case 
# script will create a data directory in this directory
# For example: /local2/psql/12/data

<pre>sh /nfs/home/chinzo/code/installation-utilities/install-postgres12.sh [/local2]</pre>

'''3. RDKIT cartridge installation'''

# You need to specify rdkit and python directory.
# /opt/rdkit is directory that you are willing to install rdkit
# /opt/python/3.6.7 is directory that you have already installed it

<pre>/nfs/home/chinzo/code/installation-utilities/install-rdkit.sh [/opt/rdkit] [/opt/python/3.6.7]</pre>

'''4. PostgreSQL12 configuration for TIN'''
<pre>sh /nfs/home/chinzo/code/installation-utilities/postgres-config.sh</pre>

[[Category:Internal]]

Tin jji

2020-04-06T22:23:52Z

Chinzo: /* install tin */

== load tin ==
<pre>
su - xyz
bash
cd /nfs/ex9/work/xyz/tin01
source /mnt/nfs/home/devtest/anaconda3/bin/activate
conda activate /nfs/soft/www/apps/tin01/envs/development
source /nfs/soft/mitools/env.sh
export TIN_HOST="n-5-35"
You can also change the port (default port is 5432)
export TIN_PORT="5432"
zincload-catalog.sh --name mce --skip-depletion H28P03.00.smi
</pre>

== install tin ==

First you need to be a root 

<pre>sudo - i</pre>

# Please replace the code with square brackets []

'''1. Python 3.6.7 installation script'''

<pre>/nfs/home/chinzo/code/installation-utilities/install-python36.sh</pre>

'''2. PostgreSQL12 installation script'''
# Please replace /local2. This is your postgres data directory. In this case 
# script will change create data directory in this directory
# For example: /local2/psql/12/data

<pre>sh /nfs/home/chinzo/code/installation-utilities/install-postgres12.sh [/local2]</pre>

'''3. RDKIT cartridge installation'''

# You need to specify rdkit and python directory.
# /opt/rdkit is directory that you are willing to install rdkit
# /opt/python/3.6.7 is directory that you have already installed it

<pre>/nfs/home/chinzo/code/installation-utilities/install-rdkit.sh [/opt/rdkit] [/opt/python/3.6.7]</pre>

'''4. PostgreSQL12 configuration for TIN'''
<pre>sh /nfs/home/chinzo/code/installation-utilities/postgres-config.sh</pre>

[[Category:Internal]]

PostgreSQL configuration

2018-11-06T19:02:23Z

Chinzo:

=='''How to tune PostgreSQL config file?'''==

Written by Chinzorig Dandarchuluun (Sep. 19, 2018).

To install pgtune by using below code

sudo yum install pgtune

Go to the PostgreSQL data folder

cd /var/lib/pgsql/9.2/data

The command will output new config file with settings roughly optimized for the server’s hardware.

pgtune -i postgresql.conf -o postgresql.conf.pgtune -T DW -c 1000

'''PG Tune Options'''
----

* -i or –input-config : Specifies the current postgresql.conf file.

* -o or –input-config : Specifies the file name for the new postgresql.conf file.

* -M or –memory: Use this parameter to specify total system memory. If not specified, pgtune will attempt to detect memory size.

* -T or –type : Specifies database type. Valid options are: DW, OLTP, Web, Mixed, Desktop

* -c or –connections: Specifies number of maximum connections expected. If not specified, it depends on database type.

* -D or –debug : Enables debugging mode.

* -S or –settings: Directory where settings data files are located at.Defaults to the directory where the script is being run from. The RPM package includes a patch to use the correct location these files were installed into.

----

Backup the current config file

sudo mv postgresql.conf postgresql.conf.backup

And then setup new config file

sudo mv postgresql.conf.pgtune postgresql.conf

Restart the server

service postgresql-9.2 restart

PostgreSQL configuration

2018-09-19T18:23:27Z

Chinzo: /* How to tune PostgreSQL config file? */

=='''How to tune PostgreSQL config file?'''==

To install pgtune by using below code

sudo yum install pgtune

Go to the PostgreSQL data folder

cd /var/lib/pgsql/9.2/data

The command will output new config file with settings roughly optimized for the server’s hardware.

pgtune -i postgresql.conf -o postgresql.conf.pgtune -T DW -c 1000

'''PG Tune Options'''
----

* -i or –input-config : Specifies the current postgresql.conf file.

* -o or –input-config : Specifies the file name for the new postgresql.conf file.

* -M or –memory: Use this parameter to specify total system memory. If not specified, pgtune will attempt to detect memory size.

* -T or –type : Specifies database type. Valid options are: DW, OLTP, Web, Mixed, Desktop

* -c or –connections: Specifies number of maximum connections expected. If not specified, it depends on database type.

* -D or –debug : Enables debugging mode.

* -S or –settings: Directory where settings data files are located at.Defaults to the directory where the script is being run from. The RPM package includes a patch to use the correct location these files were installed into.

----

Backup the current config file

sudo mv postgresql.conf postgresql.conf.backup

And then setup new config file

sudo mv postgresql.conf.pgtune postgresql.conf

Restart the server

service postgresql-9.2 restart

PostgreSQL configuration

2018-09-19T18:22:42Z

Chinzo:

=='''How to tune PostgreSQL config file?'''==

First you need install pgtune by using below code

sudo yum install pgtune

Go to the PostgreSQL data folder

cd /var/lib/pgsql/9.2/data

The command will output new config file with settings roughly optimized for the server’s hardware.

pgtune -i postgresql.conf -o postgresql.conf.pgtune -T DW -c 1000

'''PG Tune Options'''
----

* -i or –input-config : Specifies the current postgresql.conf file.

* -o or –input-config : Specifies the file name for the new postgresql.conf file.

* -M or –memory: Use this parameter to specify total system memory. If not specified, pgtune will attempt to detect memory size.

* -T or –type : Specifies database type. Valid options are: DW, OLTP, Web, Mixed, Desktop

* -c or –connections: Specifies number of maximum connections expected. If not specified, it depends on database type.

* -D or –debug : Enables debugging mode.

* -S or –settings: Directory where settings data files are located at.Defaults to the directory where the script is being run from. The RPM package includes a patch to use the correct location these files were installed into.

----

Backup the current config file

sudo mv postgresql.conf postgresql.conf.backup

And then setup new config file

sudo mv postgresql.conf.pgtune postgresql.conf

Restart the server

service postgresql-9.2 restart

PostgreSQL configuration

2018-09-19T18:20:45Z

Chinzo:

=='''How to tune PostgreSQL config file?'''==

First you need install pgtune by using below code

sudo yum install pgtune

Go to the PostgreSQL data folder

cd /var/lib/pgsql/9.2/data

The command will output new config file with settings roughly optimized for the server’s hardware.

pgtune -i postgresql.conf -o postgresql.conf.pgtune -T DW -c 1000

'''PG Tune Options'''
----

* -i or –input-config : Specifies the current postgresql.conf file.

* -o or –input-config : Specifies the file name for the new postgresql.conf file.

* -M or –memory: Use this parameter to specify total system memory. If not specified, pgtune will attempt to detect memory size.

* -T or –type : Specifies database type. Valid options are:DW, OLTP, Web, Mixed, Desktop

* -c or –connections: Specifies number of maximum connections expected. If not specified, it depends on database type.

* -D or –debug : Enables debugging mode.

* -S or –settings: Directory where settings data files are located at.Defaults to the directory where the script is being run from. The RPM package includes a patch to use the correct location these files were installed into.

----

Backup the current config file

sudo mv postgresql.conf postgresql.conf.backup

And then setup new config file

sudo mv postgresql.conf.pgtune postgresql.conf

Restart the server

service postgresql-9.2 restart

PostgreSQL configuration

2018-09-19T18:19:30Z

Chinzo:

=='''How to tune PostgreSQL config file?'''==

First you need install pgtune by using below code

sudo yum install pgtune

Go to the PostgreSQL data folder

cd /var/lib/pgsql/9.2/data

The command will output new config file with settings roughly optimized for the server’s hardware.

pgtune -i postgresql.conf -o postgresql.conf.pgtune -T DW -c 1000

'''PG Tune Options'''
----

* -i or –input-config : Specifies the current postgresql.conf file.

* -o or –input-config : Specifies the file name for the new postgresql.conf file.

* -M or –memory: Use this parameter to specify total system memory. If not specified, pgtune will attempt to detect memory size.

* -T or –type : Specifies database type. Valid options are:DW, OLTP, Web, Mixed, Desktop

* -c or –connections: Specifies number of maximum connections expected. If not specified, it depends on database type.

* -D or –debug : Enables debugging mode.

* -S or –settings: Directory where settings data files are located at.Defaults to the directory where the script is being run from. The RPM package includes a patch to use the correct location these files were installed into.

----

Backup the current config file

sudo mv postgresql.conf postgresql.conf.backup

And then setup new config file

sudo mv postgresql.conf.pgtune postgresql.conf

Restart the server

service postgresql-9.2 restart

https://www.tivix.com/blog/postgresql-no-effort-config-optimization

Group Meeting

2018-09-06T16:47:57Z

Chinzo: /* Rotation Order */

= Shoichet Lab Group Meeting Schedule =
'''Google Calendarise the Shoichet Group Meeting schedule'''
You can access the SGM schedule through your own Google calendar account by [http://www.google.com/calendar/render?cid=90hc5i060oggekk2s3c8sluf4g%40group.calendar.google.com clicking here].
For the unfortunate souls that do not have a Google account and those rebellious ones that do not care, an HTML version is available [http://www.google.com/calendar/embed?src=90hc5i060oggekk2s3c8sluf4g%40group.calendar.google.com&pvttk=b015223b9cc576dce92e6cc7698935cd here].

'''GROUP MEETINGS ARE [[FRIDAYS AT 9:30-11:00 A.M. Pacific time in GH-S536A and 12:30 to 2:00 Eastern time in Toronto]]
{{TOCright}}

= Upcoming Presentations =

*8/16/2018: Jiankun Lyu '''(Note new date Aug 16th (Thursday), and time 1-2:30 pm, in GH-N536A)'''
*8/24/2018: Christian Billesboelle
*8/31/2018: Anna Kamenik

*9/7/2018: John Irwin
*9/14/2018: no lab meeting, BKS out on Travel
*9/21/2018: Trent Balius
*9/28/2018: Ying Yang

=Rotation Order =

*Reed Stein
*Shuo Gu
*Anat Levit
*Brian Shoichet
*Aashish Manglik
*Xiaobo Wan
*Matt O'Meara
*Isha Singh
*Chase Webb
*Jiankun Lyu
*Christian Billesboelle
*John J. Irwin
*Trent Balius
*Ying Yang
*Ishan Deshpande (End of September)

*Parnian Lak (Started: 3/19/18)

*Ben R. Wong
*Chinzorig Dandarchuluun
*Supritha Amudhu
*Khanh Tang
*Jennifer Young

Holidays (NO lab meeting):
*Cesar Chavez
*Veteran's Day

There's lab mtg:
*SOP Commencement (unless BKS needs to attend)

= Room Bookings =
* GH S536A is booked by Yvonne until ... no end date - booked w/ Alma Agorilla.
[[Category:Internal]]

PostgreSQL configuration

2018-08-17T13:44:28Z

Chinzo: Blanked the page

PostgreSQL configuration

2018-08-17T13:43:57Z

Chinzo: Created page with "test"

test

User:Chinzo

2018-08-16T18:42:00Z

Chinzo:

Computer Science bachelor and graduate degree. Scientific programmer in Irwin lab. Technical skills: Java (4yrs), Android Development (3yrs), C# (3yrs), Python (1yr)