You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/cloud/04_dataproc/03_computation.md
+1-1Lines changed: 1 addition & 1 deletion
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -120,7 +120,7 @@ trino --catalog=hive
120
120
121
121
## Using Conda
122
122
123
-
NYU Dataproc comes with `miniconda3` by default. This can be used to manage Python packages within your filesystem home directory. See [here](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html) or [here](../../hpc/06_tools_and_software/04_conda_environments.mdx) for more information on the conda command.
123
+
NYU Dataproc comes with `miniconda3` by default. This can be used to manage Python packages within your filesystem home directory. See [here](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html) or [here](../../hpc/06_tools_and_software/06_conda_environments.mdx) for more information on the conda command.
Copy file name to clipboardExpand all lines: docs/hpc/03_storage/06_best_practices.md
+1-1Lines changed: 1 addition & 1 deletion
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -48,4 +48,4 @@ Your home directory has a relatively small number of inodes.
48
48
If you create a conda or python environment in you home directory, this can eat up all the inodes.
49
49
:::
50
50
51
-
Please review the [Package Management section](../06_tools_and_software/01_software_on_greene.md#package-management-for-r-python--julia-and-conda-in-general) of the [Greene Software Page](../06_tools_and_software/01_software_on_greene.md).
51
+
Please review the [Package Management section](../06_tools_and_software/01_intro.md#package-management-for-r-python--julia-and-conda-in-general) of the [Greene Software Page](../06_tools_and_software/01_intro.md).
Copy file name to clipboardExpand all lines: docs/hpc/03_storage/07_large_number_of_small_files.md
+1-1Lines changed: 1 addition & 1 deletion
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -45,7 +45,7 @@ This option may require a lot of RAM - thus you may have to wait a long time for
45
45
Special containers, which allow to either load data fast fully or access chosen elements without loading the whole dataset into RAM.
46
46
47
47
### SQLite
48
-
If you have structured data, a good option would be to use SQLite. Please see [SQLite: Handling Large Structured Data](../06_tools_and_software/05_sqlite_handling_large_structured_data.md) for more information.
48
+
If you have structured data, a good option would be to use SQLite. Please see [SQLite: Handling Large Structured Data](../06_tools_and_software/07_sqlite_handling_large_structured_data.md) for more information.
49
49
50
50
### HDF5
51
51
One can think about HDF5 file as a "container file" (database of a sort), which holds a lot of objects inside.
We encourage you to setup your own computational environment on Torch and to assist you in doing so, we allow you to run [Apptainer](../07_containers/01_intro.md) (formerly known as Singularity) containers, we manage licensed software suites and offer extensive documentation, training and support.
4
+
5
+
:::tip
6
+
We stongly advise that you setup your own computational enviromments via Apptainer containers and overlay files. Detailed documentation is available in the [containers section](../07_containers/01_intro.md).
7
+
:::
8
+
9
+
## Package Management for R, Python, & Julia, and Conda in general
Copy file name to clipboardExpand all lines: docs/hpc/06_tools_and_software/02_licensed_software.md
+18-74Lines changed: 18 additions & 74 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -1,75 +1,19 @@
1
-
# Software on Greene
2
-
3
-
## Software Overview
4
-
There are different types of software packages available
5
-
6
-
- Use `module avail` command to see preinstalled software.
7
-
- This includes the licensed software listed below
8
-
- Singularity Containers
9
-
- You can find those already built and ready to use, at location `/scratch/work/public/singularity/`
10
-
- For more information on running software with Singularity, See our [Containers Intro](../07_containers/01_intro.md).
11
-
- Python/R/Julia packages can be installed by a user
12
-
13
-
If you need another linux program installed, please contact us at [hpc@nyu.edu](mailto:hpc@nyu.edu)
14
-
15
-
## Software and Environment Modules
16
-
Lmod, an Environment Module system, is a tool for managing multiple versions and configurations of software packages and is used by many HPC centers around the world. With Environment Modules, software packages are installed away from the base system directories, and for each package, an associated modulefile describes what must be altered in a user's shell environment - such as the $PATH environment variable - in order to use the software package. The modulefile also describes dependencies and conflicts between this software package and other packages and versions.
17
-
18
-
To use a given software package, you load the corresponding module. Unloading the module afterwards cleanly undoes the changes that loading the module made to your environment, thus freeing you to use other software packages that might have conflicted with the first one.
19
-
20
-
Below is a list of modules and their associated functions:
-[Singularity for Datasets](../07_containers/04_squash_file_system_and_singularity.md)
57
-
58
-
## Licensed Software
59
-
### SCHRODINGER
1
+
# Licensed Software
2
+
3
+
## SCHRODINGER
60
4
Schrödinger provides a complete suite of software solutions with the latest advances in pharmaceutical research and computational chemistry. The NYU New York campus has a limited number of licenses for the Biologics Suite (ConfGen, Epik, Jaguar, Jaguar pKa, MacroModel, Prime, QSite, SiteMap), BioLuminate and the Basic Docking Suite.
61
5
62
6
:::note
63
7
Schrödinger can be used for non-commercial, academic purposes ONLY.
64
8
:::
65
9
66
-
####Using SCHRODINGER on HPC Cluster
10
+
### Using SCHRODINGER on HPC Cluster
67
11
68
12
To load Schrodinger module execute
69
13
```sh
70
14
$ module load schrodinger/2024.4
71
15
```
72
-
####Using SCHRODINGER on NYU Lab Computers
16
+
### Using SCHRODINGER on NYU Lab Computers
73
17
74
18
1. Request your account at: [https://www.schrodinger.com/request-account](https://www.schrodinger.com/request-account)
75
19
2. Download the software at: [https://www.schrodinger.com/downloads/releases](https://www.schrodinger.com/downloads/releases)
@@ -139,13 +83,13 @@ QSITE 5
139
83
SITEMAP 10
140
84
```
141
85
142
-
####Schrodinger Example Files
86
+
### Schrodinger Example Files
143
87
Example SBATCH jobs and outputs are available to review here:
144
88
```sh
145
89
/scratch/work/public/examples/schrodinger/
146
90
```
147
91
148
-
###COMSOL
92
+
## COMSOL
149
93
COMSOL is a problem-solving simulation environment, enforcing compatibility guarantees consistent multiphysics models. COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. The package is cross-platform (Windows, Mac, Linux). The COMSOL Desktop helps you organize your simulation by presenting a clear overview of your model at any point. It uses functional form, structure, and aesthetics as the means to achieve simplicity for modeling complex realities.
Mathematica is a general computing environment with organizing algorithmic, visualization, and user interface capabilities. The many mathematical algorithms included in Mathematica make computation easy and fast.
181
125
182
126
To run Mathematica on the Greene HPC cluster, please load the relevant module in your batch job submission script:
[MATLAB](https://www.mathworks.com/products/matlab.html) is a technical computing environment for high performance numeric computation and visualization. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an easy to use environment without using traditional programming.
245
189
246
-
####MATLAB on personal computers and laptops
190
+
### MATLAB on personal computers and laptops
247
191
248
192
NYU has a Total Academic Headcount (TAH) license which provides campus-wide access to MATLAB, Simulink, and a variety of add-on products. All faculty, researchers, and students (on any NYU campus) can use MATLAB on their personal computers and laptops and may go to the following site to download the NYU site license software free of charge.
249
193
@@ -259,10 +203,10 @@ In order to run MATLAB interactively on the cluster, [start an interactive slurm
259
203
260
204
Mathworks has provided a [Greene Matlab User Guide](https://drive.google.com/file/d/1lNNzf4lsFuH9a4bbsO18roCGhT3DwUq2/view) that presents useful tips and practices for using Matlab on the cluster.
261
205
262
-
###STATA
206
+
## STATA
263
207
Stata is a command and menu-driven software package for statistical analysis. It is available for Windows, Mac, and Linux operating systems. Most of its users work in research. Stata's capabilities include data management, statistical analysis, graphics, simulations, regression and custom programming.
264
208
265
-
####Running a parallel STATA job on HPC cluster (Greene):
209
+
### Running a parallel STATA job on HPC cluster (Greene):
266
210
267
211
To submit a STATA job for running on multiple processing elements, follow below steps.
Gaussian uses basic quantum mechanic electronic structure programs. This software is capable of handling proteins and large molecules using semi-empirical, ab initio molecular orbital (MO), density functional, and molecular mechanics calculations.
286
230
287
231
The NYU Gaussian license only covers PIs at the Washington Square Park campus. We will grant access to you after verifying your WSP affiliation. For access, please email [hpc@nyu.edu](mailto:hpc.nyu.edu).
288
232
289
-
####Running a parallel Gaussian job on HPC cluster (Greene):
233
+
### Running a parallel Gaussian job on HPC cluster (Greene):
290
234
291
235
To submit a Gaussian job for running on multiple processing elements, follow below steps.
Knitro is a commercial software package for solving large scale mathematical optimization problems. Knitro is specialized for nonlinear optimization, but also solves linear programming problems, quadratic programming problems, systems of nonlinear equations, and problems with equilibrium constraints. The unknowns in these problems must be continuous variables in continuous functions; however, functions can be convex or nonconvex. Knitro computes a numerical solution to the problem—it does not find a symbolic mathematical solution. Knitro versions 9.0.1 and 10.1.1 are available.
307
251
308
-
####Running a parallel Knitro job on HPC cluster (Greene):
252
+
### Running a parallel Knitro job on HPC cluster (Greene):
309
253
310
254
To submit a Knitro job for running on multiple processing elements, follow below steps.
Lmod, an Environment Module system, is a tool for managing multiple versions and configurations of software packages and is used by many HPC centers around the world. With Environment Modules, software packages are installed away from the base system directories, and for each package, an associated modulefile describes what must be altered in a user's shell environment - such as the $PATH environment variable - in order to use the software package. The modulefile also describes dependencies and conflicts between this software package and other packages and versions.
4
+
5
+
To use a given software package, you load the corresponding module. Unloading the module afterwards cleanly undoes the changes that loading the module made to your environment, thus freeing you to use other software packages that might have conflicted with the first one.
6
+
7
+
Below is a list of modules and their associated functions:
0 commit comments