1. Hpc Code Source Version 3. 2. 5 Ton
2. Hpc Code Source Version 3. 2. 5 Ton

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File and directory permissions

You will be responsible for setting and maintaining file permissions in your home directory and association directory. As such an understating of how Linux permissions work is crucial to the usage of Pronghorn.

General overview

Every Linux file has a set of permissions that determine whether you can read, write, or run the file. Running ls -l displays the permissions. Here's an example of such a display:

figure 1.0

The file's mode represents the file's permissions and some extra information. There are five parts to the mode.

figure 1.1

The first character of the mode (part 1) is the file type. It can be a regular file or a directory. Each file and directory has three user based permission groups which break down into three sets: user part 2, group part 3, and other part 4.

part 1: A dash (-) in this position, as in the example, denotes a regular file, meaning that there is nothing special about the file. This is by far the most common kind of file. Directories are also common and are indicated by a d in the file type slot.

part 2:user (u) - The Owner permissions apply only the owner of the file or directory, they will not impact the actions of other users.

part 3:group (g) - The Group permissions apply only to the group that has been assigned to the file or directory, they will not effect the actions of other users.

part 4:other (o) - The All Users permissions apply to all other users on the system, this is the permission group that you want to watch the most.

part 5:Directory Set Group ID - There are two special bits in the permissions field of directories.
s - Set group ID
t - Save text attribute (sticky bit) - The user may delete or modify only those files in the directory that they own or have write permission for.

Each permission set can contain four basic representations:

r : the file is readable. Refers to a user's capability to read the contents of the file.
w : the file is writable. Refers to a user's capability to write or modify a file or directory.
x : the file is executable. Refers to a user's capability to execute a file or view the contents of a directory.
s : Some executable files have an s in the user permissions listing instead of an x. This indicates that the executable is setuid, meaning that when you execute the program, it runs as though the file owner is the user instead of you. Many programs use this setuid bit to run as root in order to get the privileges they need to change system files.- : null value (nothing).

In figure 1.0 the rw- characters are the user or 'owner' permissions. rw- denotes that the files is readable and writable, but not executable. The r-- characters that follow are the group permissions. r-- denotes that the group 'examplegroup' can read, but not write or execute the file. The final r-- characters are the 'other' permissions, meaning all other users who are not the part of 'examplegroup' group or the file owner can read the file, but not write, or execute it.

Some executable files have an s in the user permissions listing instead of an x. This indicates that the executable is setuid, meaning that when you execute the program, it runs as though the file owner is the user instead of you. Many programs use this setuid bit to run as root in order to get the privileges they need to change system files. One example is the passwd program, which needs to change to /etc/passwd file.

Modifying Permissions

• chmod : Changes the file mode bits of each given file according to mode, which can be either a symbolic representation of changes to make, or an octal number representing the bit pattern for the new mode bits.
• chown : Changes the user and/or group ownership of each given file.
• chgrp : Change the group of a file or directory.

chmod
To change permissions, use the chmod command. The chmod (change mode) command protects files and directories from unauthorized users on the same system, by setting access permissions.

Some examples:

• Private file for you

• Everyone can read; you can write

• Private directory for you

• Everyone can read; you can write

chown
To change the ownership of a file(s) or directories, use the chown command. The chown (change ownership) command sets and changes the ownership of files and directories.

Some examples:

• set the ownership of myfile to mrrobot

• set the ownership of the directory and all files in mydirectory to mrrobot

chgrp
To change the group ownership of a file(s) or directories, use the chgrp command. The chgrp (change group ownership) command sets and changes the group ownership of files and directories.

Some examples:

• set the group ownership of myfile to mrrobot

• set the group ownership of the directory and all files in mydirectory to mrrobot

Videos

Topics include:

• Getting file attributes and extended attributes
• Creating and copying files and directories
• Moving and renaming files and directories
• Creating links to files and directories
• Reviewing standard Linux permissions
• Setting permissions using numeric method and symbolic method

Run

Cluster Specs

Cluster	CPU	Cores	Accelerator
6 x86 nodes	Intel(R) Xeon (R) CPU 5140 @ 2.33 GHz	4	None

Version

Cluster	HPCG Version	MPICH Version	Intel MPI
6 x86 nodes	3.0 Source	3.2	5.1.3

Makefile

MPI

We based our makefile off Make.Linux_MPI from the hpcg-3.0 source. We copied it as Make.MPI. To customize, we linked the MPI libraries properly as they were configured on the 6 node cluster.

Install/Setup Instructions

We first downloaded the tar source into our NFS folder on our MPI enabled 6 node cluster. After extracting the source, we used the following commands for setup:

Benchmarking Performance - 60 seconds

Mesh sizes must be divisible by 8.

Hpc Code Source Version 3. 2. 5 Ton

Cluster	Version	Mesh Size	Cores	GFLOP/s	Type
6 x86 nodes	3.0 Source	104	6	1.31751	MPI
6 x86 nodes	3.0 Source	16	4	1.17194	MPI
6 x86 nodes	3.0 Source	16	6	2.3234	MPI
6 x86 nodes	3.0 Source	16	24	3.44749	MPI
6 x86 nodes	3.0 Source	16	24	3.39781	MPI_OPENMPI
6 x86 nodes	3.0 Source	24	24	3.10402	MPI_OPENMPI
6 x86 nodes	3.0 Source	32	24	3.02452	MPI_OPENMPI
6 x86 nodes	3.0 Source	48	24	2.31746	MPI_OPENMPI
6 x86 nodes	3.0 Source	112	24	2.815	MPI_OPENMPI
5 x86 nodes	3.0 Source	16	20	3.11515	ICPC
5 x86 nodes	3.0 Source	24	20	2.61601	ICPC
5 x86 nodes	3.0 Source	104	20	2.34242	ICPC

Benchmarking Performance - 1 hour

Hpc Code Source Version 3. 2. 5 Ton

Cluster	Version	Mesh Size	Cores	GFLOP/s	Type
6 x86 nodes	3.0 Source	16	24	3.48752	MPI_OPENMPI