added access and getting started

Author: aatizghimire

docs/about/introduction.md

@@ -8,6 +8,7 @@ The HPC system plays a vital role in accelerating research across multiple domai
 ## Establishment and Evolution
 The **HPC cluster** was initiated on **September 1, 2018**, with support from the **Alexander von Humboldt (AvH) Foundation, Germany**, and **Higher Education Reform Project (HERP) of TU**. The system has since evolved, incorporating **multi-core CPU clusters, high-performance GPUs, and optimized software environments** for parallel computing.
 
+
 ## Objectives of TU HPC
 The TU HPC infrastructure aims to:
 
@@ -18,7 +19,7 @@ The TU HPC infrastructure aims to:
 -  **Support large-scale simulations, machine learning, and data analytics**.
 
 ## Research Domains Supported
-The HPC cluster at TU facilitates research in the following areas:
+The HPC cluster at TU facilitates currently working on research in the following areas:
 
 -  **Condensed Matter Physics**: First-principles calculations and quantum simulations.
 -  **Artificial Intelligence & Machine Learning**: Training and deploying deep learning models.

docs/access/registration.md

@@ -0,0 +1,43 @@
+Access to the **Tribhuvan University HPC system** is granted to **researchers, faculty, students, and industry collaborators** who require high-performance computing resources for **scientific research and computational projects**. The registration process ensures that users have a **valid research proposal and appropriate infrastructure needs**.
+
+## Registration Process
+To request access to TU HPC, follow these steps:
+
+### **1. Prepare a Research Proposal**
+Applicants must submit a **detailed research proposal** that includes:
+
+- **Research title and objectives**
+- **Computational requirements (CPU, GPU, software dependencies, storage needs, etc.)**
+- **Expected duration of HPC usage**
+- **Potential research impact and outcomes**
+
+### **2. Recommendation Letter (For Undergraduate Students)**
+Undergraduate students must provide a **recommendation letter** from:
+
+- A **faculty advisor or supervisor** supporting their research project.
+- The letter should highlight the **student’s capability and need for HPC resources**.
+
+### **3. Send an Email Request**
+Applicants should email their request to **Dr. Madhav Prasad Ghimire** at:
+
+📩 **[madhav [dot] ghimire @ cdp [dot] tu [dot] edu [dot] np](mailto:)**
+
+The email should include:
+
+- **Research proposal (PDF format)**
+- **Recommendation letter (if applicable)**
+- **Requested infrastructure details**
+
+### **4. Review & Approval**
+- The **HPC administration team** will review applications.
+- Approved users will receive an **HPC account and login credentials**.
+- Users must **agree to the HPC usage policies** before accessing the system.
+
+## Important Notes
+- **Only approved research projects will be granted access**.
+- **HPC resources are limited**, so users must request only what they require.
+- Users must **renew access periodically** based on project requirements.
+
+For any inquiries or support, contact **[madhav [dot] ghimire @ cdp [dot] tu [dot] edu [dot] np](mailto:)**.
+
+> _Enabling researchers with high-performance computing power!_ 🚀

docs/access/roles.md

@@ -0,0 +1,46 @@
+## User Roles
+The following user roles define access levels and responsibilities within the HPC system:
+
+### **1. HPC Administrators**
+- Responsible for **system management, maintenance, and user support**.
+- Have full access to **all system configurations, job scheduling, and software installations**.
+- Manage **network security, storage, and system upgrades**.
+
+### **2. Faculty & Principal Investigators (PIs)**
+- Can **request access for research projects and student users**.
+- Have **priority access** to HPC resources for approved projects.
+- Allowed to install **custom software** upon request.
+- Responsible for **ensuring ethical usage of HPC resources**.
+
+### **3. Research Scholars & Graduate Students**
+- Can submit **jobs to compute nodes** and use **available software**.
+- Allowed to use **scratch storage for temporary data processing**.
+- Must follow **fair usage policies** to ensure equitable resource distribution.
+
+### **4. Undergraduate Students**
+- Allowed access **only under supervision** of a faculty member or PI.
+- Required to submit a **recommendation letter** to gain access.
+- Can perform **basic computations and coursework-related HPC tasks**.
+
+### **5. External Collaborators & Industry Users**
+- Can access **HPC resources through joint research projects**.
+- Require **prior approval** from the **HPC administration team**.
+- Access is **time-limited and subject to specific project needs**.
+
+## Permissions & Access Levels
+The table below outlines the **access privileges** for each user role:
+
+| Permission                     | Admins | Faculty/PIs | Researchers | Undergraduates | Industry Users |
+|--------------------------------|--------|------------|-------------|----------------|----------------|
+| Submit Jobs to Compute Nodes   | ✅      | ✅          | ✅           | ✅ (Limited)    | ✅ (Limited)    |
+| Access Scratch Storage         | ✅      | ✅          | ✅           | ✅ (Limited)    | ✅              |
+| Install Custom Software        | ✅      | ✅ (Approval Required) | ❌ | ❌ | ❌ |
+| Modify SLURM Job Scheduler     | ✅      | ❌          | ❌           | ❌              | ❌              |
+| Request Additional Resources   | ✅      | ✅          | ✅ (Limited) | ❌              | ✅              |
+| Long-term Storage Allocation   | ✅      | ✅          | ✅ (Approval Required) | ❌ | ✅ |
+
+## Policy Compliance & Violations
+Users must comply with **HPC policies** regarding **fair usage, security, and data privacy**. Violations such as **misuse of resources, unauthorized software installations, or security breaches** may result in **account suspension or permanent revocation of access**.
+
+
+> _Ensuring responsible and efficient use of HPC resources!_ 🚀

docs/access/security.md

@@ -0,0 +1,46 @@
+The **HPC system at Tribhuvan University** follows **strict security policies** to ensure **data integrity, system stability, and secure access**. All users must follow these security guidelines to maintain a **safe computing environment**.
+
+## 1. User Authentication & Access Control
+- **SSH Key-Based Authentication**: Users must use **SSH keys** for remote access; password-based authentication is disabled.
+- **Multi-Factor Authentication (MFA)**: If enabled, users must follow the additional authentication steps.
+- **User Account Management**:
+  - Each user must have a unique account.
+  - **Sharing credentials is strictly prohibited**.
+  - Users must update their passwords regularly and use **strong password policies**.
+
+## 2. Data Security & Privacy
+- Users must **not store sensitive personal data** or proprietary research data without encryption.
+- All data must be stored in **designated directories** (`/home`, `/mnt/storage0`) following storage policies.
+- **Data backups are the responsibility of the users**; the HPC system provides limited backup capabilities.
+- Users should not share or transfer research data without appropriate permissions.
+
+## 3. Network & Remote Access Security
+- The HPC system is hosted at **ITIC Tribhuvan University**, and **NAT is managed by TU ITIC and the Registrar Office**.
+- **Only authorized users can access the system remotely via SSH**.
+- **Public-facing services are restricted**; users cannot expose any services without administrator approval.
+- **No unauthorized VPNs, proxies, or tunneling methods** should be used.
+
+## 4. Software Installation & Execution Policies
+- Users **cannot install system-level software** without approval.
+- All software requests should be made via **[madhav [dot] ghimire @ cdp [dot] tu [dot] edu [dot] np]**.
+- Executable files must be **scanned for security risks** before running.
+- Users must **not run scripts that consume excessive resources** or cause instability.
+
+## 5. Job Submission & Fair Usage
+- Users must ensure **efficient job scheduling** and avoid unnecessary resource hogging.
+- Long-running jobs must be **checked and optimized** to minimize impact on shared resources.
+- **Priority scheduling is based on fair usage policies**; abusing the system may result in restricted access.
+
+## 6. Incident Reporting & Policy Violations
+- Users must report **security incidents or suspicious activities** immediately to **support**.
+- Violations of security policies may result in **temporary or permanent suspension**.
+- Regular audits are conducted to monitor compliance and ensure the integrity of the HPC system.
+
+## 7. Future Security Enhancements
+- Implementation of **enhanced network monitoring tools**.
+- Regular **security awareness training** for users.
+- Exploring **VPN-based secure access for external researchers**.
+
+For any security concerns or questions, contact **[madhav [dot] ghimire @ cdp [dot] tu [dot] edu [dot] np](mailto:)**.
+
+> _Ensuring a secure and high-performance computing environment!_ 🔒🚀

docs/access/who_can_access.md

@@ -0,0 +1,48 @@
+
+The **HPC system at Tribhuvan University** is designed to support **researchers, faculty, and students** engaged in computational research. Access to the HPC infrastructure is **available to national and international collaborators**, subject to approval by the TU HPC administration.
+
+## Eligible Users
+The following groups are eligible to apply for access to TU HPC:
+
+### **1. Faculty & Researchers**
+- Professors and researchers affiliated with **Tribhuvan University and other academic institutions** in Nepal.
+- Researchers from **national and international universities collaborating with TU**.
+- Scientists working on **HPC-based projects in material science, AI, computational physics, and related fields** from **Nepal**.
+
+### **2. Students (Graduate & Undergraduate)**
+- **Master’s and Ph.D. students** conducting research that requires high-performance computing.
+- Undergraduate students participating in **HPC-related coursework, projects, or internships**.
+- Students must be supervised by an **approved faculty advisor or research group**.
+
+### **3. Government & Industry Collaborators**
+- Researchers from **government organizations** requiring computational resources for policy planning, climate modeling, or engineering simulations.
+- **Industry partners and startups** engaged in AI research, data analytics, and scientific computing.
+- Collaborators involved in **joint projects with TU HPC or AMRL research groups**.
+
+### **4. Independent & International Researchers**
+- Independent researchers may request access for **specific, well-defined projects** from **Nepalese** Origin.
+- International collaborations are welcome, subject to approval and partnership agreements.
+
+## How to Apply for Access
+To gain access to the TU HPC system, users must:
+
+1. **Submit an HPC Access Request**
+   - Fill out the application form available at **[TU HPC Registration](../access/registration.md)**.
+   - Include details of your research project and computing requirements.
+
+2. **Approval & Account Creation**
+   - Applications will be reviewed by the **HPC administration team**.
+   - Approved users will receive login credentials and access instructions.
+
+3. **Comply with HPC Usage Policies**
+   - Users must adhere to the **HPC code of conduct and fair usage policies**.
+   - Violations of policies may result in account suspension.
+
+## Acknowledging TU HPC in Research
+Users publishing research that utilizes **TU HPC resources** must acknowledge the infrastructure in their publications:
+
+> "This research acknowledges IFW-Dresden for providing the large-scale compute nodes to Tribhuvan University for scientific computations."
+
+For more details on applying for access, visit the [HPC Access Guide](../access/registration.md) or contact **[madhav [dot] ghimire @ cdp [dot] tu [dot] edu [dot] np](mailto:)**.
+
+> _Providing equitable access to high-performance computing for Nepal's research community!_ 🚀

docs/getting_started/file_transfer.md

@@ -0,0 +1,77 @@
+Users working on **TU HPC** need to transfer files between their local systems and the HPC cluster. **Globus is not available**, so users must use standard **secure file transfer methods** like `scp`, `rsync`, and `sftp` for **safe and efficient data transfer**.
+
+## 1. Secure File Transfer Using SCP
+The `scp` (Secure Copy Protocol) command allows users to copy files **securely over SSH**.
+
+### **Uploading a File to HPC**
+From your local machine, use:
+```bash
+scp myfile.txt username@tu-hpc-ip:/home/username/
+```
+This copies `myfile.txt` from your local system to your **home directory** on TU HPC.
+
+### **Downloading a File from HPC**
+```bash
+scp username@tu-hpc-ip:/home/username/myfile.txt ./
+```
+This downloads `myfile.txt` from the HPC system to your local system.
+
+### **Transferring Entire Directories**
+```bash
+scp -r myfolder username@tu-hpc-ip:/home/username/
+```
+The `-r` flag copies entire directories recursively.
+
+## 2. Efficient File Transfer with Rsync
+For **resumable and optimized** file transfers, `rsync` is recommended.
+
+### **Uploading a Directory with Rsync**
+```bash
+rsync -avz myfolder username@tu-hpc-ip:/home/username/
+```
+The `-a` (archive), `-v` (verbose), and `-z` (compression) flags ensure efficient transfer.
+
+### **Downloading Files Using Rsync**
+```bash
+rsync -avz username@tu-hpc-ip:/home/username/myfolder ./
+```
+If a transfer is interrupted, simply rerun the same command to resume from where it left off.
+
+## 3. Interactive File Transfer with SFTP
+For interactive file transfers, use `sftp`:
+```bash
+sftp username@tu-hpc-ip
+```
+Once connected, use:
+- `put myfile.txt` (Upload file to HPC)
+- `get myfile.txt` (Download file from HPC)
+- `ls` (List remote files)
+- `bye` (Exit SFTP session)
+
+## 4. Large File Transfers & Storage Guidelines
+- **Use Rsync** for large datasets to avoid re-transfers of unchanged files.
+- Store files in **appropriate directories** (`/home/username/` for personal data, `/mnt/storage0/` for temporary large-scale computations).
+- **Do not store unnecessary files** in `/home/`, as space is limited.
+
+## 5. Automating File Transfers
+To automate regular file transfers, add your SSH key for passwordless authentication and create a cron job:
+```bash
+crontab -e
+```
+Example cron job to sync a folder daily at midnight:
+```bash
+0 0 * * * rsync -avz /local/folder username@tu-hpc-ip:/home/username/
+```
+
+## 6. Troubleshooting File Transfers
+- If `scp` or `rsync` is slow, try adding `-e "ssh -C"` for compression:
+```bash
+scp -C myfile.txt username@tu-hpc-ip:/home/username/
+```
+- If the connection fails, ensure your **SSH keys** are correctly set up.
+- Check available space using:
+```bash
+df -h
+```
+
+> _Efficient and secure file transfer for HPC workflows!_ 🚀

docs/getting_started/first_job.md

@@ -0,0 +1,87 @@
+After gaining access to the **HPC system at Tribhuvan University**, users can submit jobs using the **SLURM job scheduler**. This guide explains how to run your first job, monitor its status, and optimize job submissions.
+
+## 1. Logging into the HPC System
+Before running jobs, connect to the TU HPC system via SSH:
+```bash
+ssh username@tu-hpc-ip
+```
+Ensure you are in your **home directory** or an appropriate project folder before submitting jobs.
+
+## 2. Creating a SLURM Job Script
+A job script tells the **SLURM scheduler** how to allocate resources and execute your program. Create a job script (e.g., `job.slurm`) using a text editor:
+```bash
+nano job.slurm
+```
+Add the following SLURM directives to specify job parameters:
+```bash
+#!/bin/bash
+#SBATCH --job-name=test_job  # Job name
+#SBATCH --output=output.txt  # Output file
+#SBATCH --error=error.log    # Error file
+#SBATCH --ntasks=1           # Number of tasks
+#SBATCH --cpus-per-task=4    # Number of CPU cores per task
+#SBATCH --time=01:00:00      # Time limit (hh:mm:ss)
+#SBATCH --partition=normal   # Specify partition (e.g., normal, protein, fplo)
+
+module load python/3.10.12   # Load required module
+python my_script.py          # Run Python script
+```
+Save and exit (`CTRL + X`, then `Y` and `ENTER`).
+
+## 3. Submitting the Job
+Submit the job to the SLURM scheduler using:
+```bash
+sbatch job.slurm
+```
+This will add your job to the queue, and it will execute once resources are available.
+
+## 4. Monitoring Job Status
+To check the status of your submitted jobs, use:
+```bash
+squeue -u $USER
+```
+To view detailed job information:
+```bash
+scontrol show job <job_id>
+```
+To cancel a job:
+```bash
+scancel <job_id>
+```
+
+## 5. Checking Job Output
+Once the job is completed, check the output and error files:
+```bash
+cat output.txt  # View job output
+cat error.log   # View error messages (if any)
+```
+
+## 6. Optimizing Job Submissions
+- Use **appropriate resource allocation** (CPU, memory, and time) to avoid long queue times.
+- Run **test jobs** with small datasets before scaling up computations.
+- Use **job dependencies** if running multiple interdependent tasks:
+```bash
+sbatch --dependency=afterok:<job_id> job2.slurm
+```
+- Consider using **parallel computing** (MPI, OpenMP) for efficiency.
+
+## 7. Example: Running a GPU Job
+For GPU-based workloads, modify the script as follows:
+```bash
+#!/bin/bash
+#SBATCH --job-name=gpu_test
+#SBATCH --output=gpu_output.txt
+#SBATCH --gres=gpu:1        # Request 1 GPU
+#SBATCH --partition=protein # Use GPU-enabled partition
+
+module load cuda/11.2
+./gpu_program
+
+```
+Submit it using:
+
+```bash
+sbatch gpu_job.slurm
+```
+
+> _Start computing efficiently on TU HPC!_ 🚀

docs/getting_started/access.md docs/getting_started/ssh.mddocs/getting_started/access.md renamed to docs/getting_started/ssh.md

@@ -51,8 +51,4 @@ Type : yes, otherwise the system will disconnet.
 
 Note: The typed password is invisible in terminal.
 
-## Forgot Password?
-
-Please raise a ticket regarding this issue under  User Support  and the system administrator will resolve your problem. 
-
-
+> _Enabling researchers with high-performance computing power!_ 🚀