Fortran Resources (recipes, libraries, learning materials, etc)

Fortran95 features
from Wikipedia

List of Fortran Numerical Libraries
from Wikipedia

Numerical Methods for Fortran Programmars
from people.sc.fsu.edu
contain links to fortran libraries and subroutines

Scientific Programming and Numerical Computation
from Wu-ting Tsai, National Taiwan University.

Fortran95 Interface to Matlab
from Matlab

Fortran Resources List
from BCS Fortran Specialist Group

Fortran Wiki
contains tutorials and FORTRAN code collections
contains list of links that contain FORTRAN codes

Fortran Tutorials ( a list of tutorials)
a list form The Fortran Company

Computational Physics using Fortran (official link)
an NPTEL course with a brief introduction to Fortran

Fortran90 Tutorial 
From MTU

Python blogs follow

https://scientific-python-101.readthedocs.io/numpy/math.html

List of Lists (Wikipedia)

Principles
Paradoxes
List of Unsolved Problems (all area)
Unsolved Problems in Physics
Unsolved Problems in Mathematics
Unsolved Problems in Astronomy
Unsolved Problems in Chemistry
Unsolved Problems in Biology
Undecidable Problems
Fundamental theorem
Conjectures

News sites, scientific magazines and education journals in science

Patents Search
Wipo National Database
Free Patents Online (FPO)
Google Patents
USPTO
InPass
Espacenet
PatentScope


Review Journals
Annual Reviews
Chemical Reviews (ACS)
Chemical Society Reviews (RSC)
Reviews in Modern Physics
Nature Reviews


News Sites
Nature News and Views
Science News
Chemical & Engineering News (c&en)
Physics World (IOP Publishing)
India Science Wire
Laboratory News
The Scientist
MIT Technology Review

Magazines
Current Science
Physics Today
Science Reporter
Scientific American
Chemistry World
Symmetry Magazine
Physics World
Quanta Magazine
Australian Science
Dream2047
New Scientist

Education Journals
American Journal of Physics
Resonance
Journal of Chemical Education
European Journal of Physics
Physics Today


Computational Journals
Journal of Computational Physics (and X)
Computer Physics Communications
Computational Science (Nature)



More on this list
Google Scholar Metric list

Checking the status of the submitted job in HPC

The submitted jobs in PBS queue system can be checked whether they are in queue still, or running, or completed, etc. The command to use (in PBS software) is qstate.

Job id            Name             User              Time Use S Queue
----------------  ---------------- ----------------  -------- - -----
306.clr     jobname              user              10:36:59 R worke

Commands to use are:
qstat    (lists all the jobs with some details)
qstat -n  (list all the jobs with total number of CPUs running the jobs
qstat -u user (list all the jobs submitted by the user)


To see a list of things to know (for a newbie) to use high performance cluster, click here. 

Best sites for Physics (and other things) Discussion

Stack Exchange (for basic questions)

Stack Exchange Overflow sites (for advanced questions)

Physics Forums

Socratic 

Reddit

To run jobs in specific node in a HPC cluster

Some time, you may want to run a job in a specific folder. For example, to check if all the nodes are working properly after restarting the cluster.

1. Use #PBS -Wall to mention the name

A simplest way is to run as many number of jobs as that of the node at the same time (which can take some time to complete) and use

qstat -n 

to see whether all the nodes are used for the calculation.

To see all the nodes in a cluster, use
pbsnodes -a

cluster
     Mom = headnodename.companyname
     ntype = PBS
     state = free
     pcpus = 24
     resources_available.arch = linux
     resources_available.host = cluster
     resources_available.mem = 264417884kb
     resources_available.ncpus = 24
     resources_available.vnode = cluster
     resources_assigned.accelerator_memory = 0kb
     resources_assigned.mem = 0kb
     resources_assigned.naccelerators = 0
     resources_assigned.ncpus = 0
     resources_assigned.netwins = 0
     resources_assigned.vmem = 0kb
     resv_enable = True
     sharing = default_shared

cn1
     Mom = cn2.aracluster
     ntype = PBS
     state = free
     pcpus = 24
     resources_available.arch = linux
     resources_available.host = cn2
     resources_available.mem = 264424324kb
     resources_available.ncpus = 24
     resources_available.vnode = cn2
     resources_assigned.accelerator_memory = 0kb
     resources_assigned.mem = 0kb
     resources_assigned.naccelerators = 0
     resources_assigned.ncpus = 0
     resources_assigned.netwins = 0
     resources_assigned.vmem = 0kb
     resv_enable = True
     sharing = default_shared

cn2
     Mom = cn1.aracluster
     ntype = PBS
     state = free
     pcpus = 24
     resources_available.arch = linux
     resources_available.host = cn1
     resources_available.mem = 264424336kb
     resources_available.ncpus = 24
     resources_available.vnode = cn1
     resources_assigned.accelerator_memory = 0kb
     resources_assigned.mem = 0kb
     resources_assigned.naccelerators = 0
     resources_assigned.ncpus = 0
     resources_assigned.netwins = 0
     resources_assigned.vmem = 0kb
     resv_enable = True
     sharing = default_shared

Here, cn1, cn2 are the nodenames. The first one 'cluster' is the name of the head node.

Mentions these names in the #PBS option. For example,

#PBS -l nodes=cn1;ncpus=4

This option will run 4 cpus from cn1 node in the cluster.

=======================================================
You can use

cat /etc/hosts

to display the nodenames.

Click here to go back to "Important things to before you work on HPC cluster"

Important things to before you work on High Performance Computing (HPC) cluster: For Beginners

1. Why HPC is important and where it is used?
2. For login, use ssh login and use bitvise ssh client from windows
3. See the default shell, echo '$0' or echo '$SHELL' 
4. Which Scheduling software is used by the cluster?
5. Changing user privileges (chmod)  
6. Copying files or directories from a cluster to local and vice-versa
7. List all the compilers in the cluster
8. List the number nodes in the cluster
9. To see the OS, type, bit, etc. 
10. List the active and dead nodes
11. Submit jobs to PBS que (qsub)
12. How to submit multiple jobs using qsub?
13. See the status of the submitted job (qstat)
14. Terminating a Job (qdel)
15. Run a job in a specific node
16. What is mean by compiling serially
17. What is mean by compiling parallel
18. Compiling C, C++ and Fortran code using gnu/intel compilers
19. Using make: configure, make and make install
20. List of commands need to use sheduler
21. How to check the size of files/files 
22. How to check disk space used and free
23. Working with BLAS library
24. Working with LAPACK library
25. Working with OpenMP
26. Working with Intel Fortran + MKL Libraries
27. Working with Intel Fortran Compiler Cluster edition 
28. Working with FFTW library
29. Fortran usage
30. C usage
31. C++ usage
32. Python usage
33. Using watch command to see the changes on the screen
34. List of Scripts to work with HPC, cluster, supercomputer

Note: Add your suggestion on what you want to add here. We will add them in future.

List of numerical libraries used in Quantum Chemistry / Computational Materials Science codes

The speed of a quantum chemical calculation often depends on how efficient the used numerical libraries are. Here is a list of numerical libraries that are widely used in various scientific codes.

C Program based
FFTW
GNU Scientific Libarary
Intel MKL (includes BLAS, LAPACK, ScaLAPACK, FFT, etc)

C++ Program based
Armadillo
LAPACK++
Intel MKL

Fortran Program based
LAPACK
LINPACK
Netlib

Python Program based
NumPy
SciPy
ScientificPython
SymPy

How to do research Series (1/100)

Four golden lessons

by Prof. Steven Weinberg, Nobel Laureate in Physics (from Nature article)

Rule #1:

"I managed to get a quick PhD — though when I got it I knew almost nothing about physics. But I did learn one big thing: that no one knows everything, and you don't have to."


Rule #2:

"When I was teaching at the Massachusetts Institute of Technology in the late 1960s, a student told me that he wanted to go into general relativity rather than the area I was working on, elementary particle physics, because the principles of the former were well known, while the latter seemed like a mess to him. It struck me that he had just given a perfectly good reason for doing the opposite."

"My advice is to go for the messes — that's where the action is."

Rule #3:

It is to forgive yourself for wasting time. As you will never be sure which are the right problems to work on, most of the time that you spend in the laboratory or at your desk will be wasted. If you want to be creative, then you will have to get used to spending most of your time not being creative, to being becalmed on the ocean of scientific knowledge.

Rule #4:

Finally, learn something about the history of science, or at a minimum the history of your own branch of science. You can get great satisfaction by recognizing that your work in science is a part of history.

Reference:

These are extracted from: S. Wienberg, Scientist: Four golden lessons, Nature 426, 389 (27 November 2003) | doi:10.1038/426389a

Things to do when you leave your PC Series - Part 1

Now a days, it is normal to upgrade to a new PC. In older PC, we may use a lot of things such as synchronizing browsers, installing Dropbox etc.

• Before abandon old systems, these things have to be given much importance. The update link to such systems should be removed (especially for Dropbox etc).

• 
  
• Need to uninstall important personal packages. If some one is interested in a package, let them install the package again.

If you are using Mendeley, click here to read related to Medeley desktop.

(will be updated soon...)

Tools for a Scientific Code Developer

Through reading, I understand that following skills are essential for a researcher who write code.

Apart from a good command in Linux OS and bash scripting, I understand that coding ability using following languages is essential.

1. Python 
2. C and C++
3. Fortran

Following sites are useful

Stackexchange 

        In this site, I like Academia, StackOverflow, Unix & Linux etc. The good aspect I like is that you will get excellent answers.

GitHub Repository   

          One can use this site for version control of the code development.


Regular Expression 

       Regular expression is a key skill for a programmer. This regexr.com https://regexr.com/ provides a userfriendly plaform to learn and build REGEX expressions.