# hlajungo - HiPac 3 Release Note and informations
[HiPac 3 Release Note and informations](https://hackmd.io/2deAUP8zQ-u1giVioCOdaQ)
mail `[e-mail]`

## Toturial

[passwordless ssh](/IcmO9G86TaOG3cLXogdtlg)
[Set NFS](/vJkijTgZRDepNAxaefxhWw)
[Set NIS](/QtmjczrDR-qbGUeo5VNC4w)
[Install Mellanox OFED Driver-24.04-0.7.0.0](/XV0ElHwhRTSpor-5CjzV9A)
[Install any version of NVidia driver and cuda on ubuntu](/-jpp8JUHSMC48ATFkn1vgQ)

[Sending mail on ubuntu-22.04](/TKOwtY0FTRO4ogB6A3L60g)
[Crontab](/cY8RX5FqTP28QaRZYGX64A)

[Control gcc & g++ version](/uD3UhFnDSD6CrPm744F9gA)
[Install icc-2021.4.0 ](/JZ2F8BTYRu6V0zYJ3_Fs0A)
[Install mkl](/n5RgUwJQSly83KjnEibhbw)
[Compile NAMD-2.14](/DJiz9UAJTrO6dsjyPI0cSw)
[NAMD-2.14 parameter](/UJWIJB5-RFCcEkt-zrP-Zw)

<!--
Using Conda to manage CUDA is very recommend.
[Conda](/qVODoabFTCa1Z-eeqGsECw)
-->
[Install basic](/xD-E0c5AQtStPWFtiND3eA)
[Some useful terminal commands](/OfgAxYMCSIGXOnZCTemqlw)

[Mount disk at boot](/6TsN2arQQiCZGEoTiFyAMQ)

## Resource Collected

### NAMD2
#### Data
To run NAMD2, you need pdb, psf, force field(CHARMM or XPLOR) and a configure file
[NAMD Sample](http://www.ks.uiuc.edu/Research/namd/utilities/)
[Protein Data Bank Japan](https://hackmd.io/SBx54czZSqq7Zl17JDvr_g)
[Protein Data Bank RCSB](https://www.rcsb.org/)
[CHARMM forcefield](http://mackerell.umaryland.edu/charmm_ff.shtml#charmm)

#### Build
NOTE: For building or config ,best Resource is `./build --help` or `./config`, it will give you all the information you need.
- [NAMD 2.14 Release Note (Compile NAMD)](http://www.ks.uiuc.edu/Research/namd/2.14/notes.html)
### Video Toturial
[Youtube VMD toturial](https://www.youtube.com/watch?v=mi6fZLrcZM8&list=PLhYF9QNr23IaG-aFub24_T8XnIbJb7fNU&index=2)
[NVidia Video](https://info.nvidia.com/NALA_DEV_WBN_201605_NAMD_Webinar_Conf_Page_On_Demand.html)

### Offical Documentation
#### Mellanox OFED
[Mellanox OFED User Guide 24.04-0.7.0.0 Ubuntu 22.04 x86_64](https://docs.nvidia.com/networking/display/mlnxofedv24040700/user+manual)
[Mellanox OFED release note 24.04-0.7.0.0 Ubuntu 22.04 x86_64](https://docs.nvidia.com/networking/display/mlnxofedv24040700/release+notes)
#### Charm++
[Charm++ GitHub page](https://github.com/UIUC-PPL/charm)
[Charm++ Official](https://charm.cs.illinois.edu/software)
[Charm++ User Guide](https://charm.readthedocs.io/en/latest/charm++/manual.html)
### Article
[NVidia NAMD2 Performance blog](https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/)
[NVidia NAMD Toturial](https://www.nvidia.com/es-la/data-center/gpu-accelerated-applications/namd/)

<!--
## Script
You need a script to move generated binary

A script that take arguments to seting
--binary-prefix /path/to/binary/ \
--binary binary \
--cpunum 10 \
--gpunum 7
--other-argument "+cpuaff..."

[argument ], .namd file, and auto write result to a file

### Test Namd

#!/bin/bash

#######################
# sleep between each run
#######################
sleep_between_run=20
#Data
testname_dir="/home/hlajungo/Downloads/biomedcases/case_01/inData"
#Configure file
namd2_configure_file="/home/hlajungo/Downloads/biomedcases/case_01/cpu/md.namd"
#binary dir
namd2_bin_dir="/media/hlajungo/新增磁碟區/linux/namd-2.14/namd-2.14_bin"

namd_log_file="md.out"
data_file_nsday="namd2_data_nsday"


# Create necessary directories
mkdir -p "./output"


# Run namd2 for each subdirectory
subdirs=("$namd2_bin_dir"/*)
num_subdirs=${#subdirs[@]}

subdir="${subdirs[0]}"
CHARMRUN="$subdir/charmrun"
NAMD2="$subdir/namd2"
CMD_OPTIONS="+p30 +setcpuaffinity +idlepoll +devices 0"
namd_command="$CHARMRUN $NAMD2 $CMD_OPTIONS $namd2_configure_file"


eval "$namd_command" > /dev/null 2>&1
sleep $sleep_between_run

for ((i=0; i<num_subdirs; i++)); do
    subdir="${subdirs[i]}"
    if [ -d "$subdir" ]; then
        CHARMRUN="$subdir/charmrun"
        NAMD2="$subdir/namd2"
        CMD_OPTIONS="+p14 +setcpuaffinity +idlepoll"
        #CMD_OPTIONS="$CMD_OPTIONS +devices 0"
        namd_command="$CHARMRUN $NAMD2 $CMD_OPTIONS $namd2_configure_file"

        #echo "$namd_command"
        eval "$namd_command" > "$namd_log_file"

        sum_ns_per_day=0
        count=0
        days_per_ns_list=$(grep "Benchmark" "$namd_log_file" | grep -oP '\d+(\.\d+)?(?= days/ns)')
        for days_per_ns in $days_per_ns_list; do
            ns_per_day=$(echo "scale=6; 1 / $days_per_ns" | bc)
            sum_ns_per_day=$(echo "$sum_ns_per_day + $ns_per_day" | bc)
            count=$((count + 1))
        done

        subdir_noprefix="${subdir/#$namd2_bin_dir}"

        if (( count > 0 )); then
            avg_ns_per_day=$(echo "scale=6; $sum_ns_per_day / $count" | bc)
            echo "$avg_ns_per_day $subdir_noprefix" >> "$data_file_nsday"
        else
            echo "File $namd_log_file: no valid days/ns values found"
        fi

        if [ $i -ne $((num_subdirs - 1)) ]; then
           sleep $sleep_between_run
        fi
    fi
done

eval "$namd_command" > /dev/null 2>&1

sort -nr "$data_file_nsday" > "${data_file_nsday}_sorted"

cat "$data_file_nsday"

rm -rf "./output"
rm "$data_file_nsday"
rm "${data_file_nsday}_sorted"

-->