Year: 2018

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Checking and Modifying Timestamp of whole Directory recursively

Step 1: Show the complete date, time and year for a specific file

$ ls -l --full-time
-rwxrwxr-x  1 root root  1109 2018-07-20 12:52:52.587945000 +0800 Allwmake
drwxrwxr-x  5 root root  4096 2018-07-20 12:52:52.602945000 +0800 applications
drwxrwxr-x  3 root root  8192 2018-07-20 12:53:19.536973000 +0800 bin
-rw-rw-r--  1 root root 35646 2018-07-20 12:52:52.592945000 +0800 COPYING
drwxrwxr-x  5 root root  4096 2018-07-20 12:53:19.936974000 +0800 doc
drwxrwxr-x  8 root root  4096 2018-07-20 12:53:20.039974000 +0800 etc
drwxr-xr-x  4 root root  4096 2018-07-20 12:55:17.230101000 +0800 platforms
-rw-rw-r--  1 root root  1620 2018-07-20 12:52:52.597945000 +0800 README.org
drwxrwxr-x 38 root root  4096 2018-07-20 12:53:22.032976000 +0800 src
drwxrwxr-x 17 root root  4096 2018-07-20 12:54:45.114064000 +0800 tutorials
drwxrwxr-x  7 root root  4096 2018-07-20 12:55:15.939099000 +0800 wmake

Step 2: If you wish to modify the time-stamp for the entire directory, you can use the command,

% for file in `find .`; do touch $file; done

References:

  1. touch – change file timestamps(Unix Tutorial)
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Resolving Orphaned Objects in Centrify Access Manager

On the Centrify Access Manager, when we search for the userid, the Centrify Access Manager is not found.
But when we add the userid in the system, it mentioned that the userid is duplicated. It seems that the userid has been cached and orphaned somewhere in Centrify.

Step 1: To find out duplicated users / objects, you may use Analyze feature in Access Manager. See Pix 1

Step 2: Analyse Results

You will notice

– Duplicate users in zones
– Orphan zone data objects and invalid data links

Step 3: Right-Clicked to fix the isses

You should be able to add the user.

 

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Formatting NVME Partition on CentOS 7

Step 1: Create a partition:

# sudo fdisk /dev/nvme0n1
Choose “n” to create a new partition
Then "p" and "1" for new partition
Using default paratmeter, "w" to write data to disk

Step 2: Create a file system on it:

# sudo mkfs -t ext4 /dev/nvme0n1p1

Step 3: Create a mount point somewhere convenient:

# sudo mkdir /media/nvme

Step 4: Mount the new partition on that mount point:

# sudo mount /dev/nvme0n1p1 /media/nvme

Step 5: Permanently Mount the Device
Step 5a. To find the UUID first

# sudo blkid

Step 5b: To get it to mount every time, add a line to /etc/fstab:

UUID=nvme_UUID /media/nvme ext4 defaults 0 0

(where nvme_UUID is the value taken from “sudo blkid”)

Step 6 (Optional): At this point, the whole thing belongs to ‘root’

To change the ownership to a specific user (with the partition mounted):

# sudo chown -R user:usergroup /media/nvme
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Nvidia Tesla versus Nvidia GTX Cards

References

  1. Performance Comparison between NVIDIA’s GeForce GTX 1080 and Tesla P100 for Deep Learning
  2. Comparison of NVIDIA Tesla/Quadro and NVIDIA GeForce GPUs

 

Nvidia EULA

Key clauses are: 2.1.3 that states no DC deployment, commercial hosting and broadcast services
http://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us&type=GeForce

 

FP64 64-bits (Double Precision) Floating Point Calculation


Pix taken from Comparison of NVIDIA Tesla/Quadro and NVIDIA GeForce GPUs

FP16-16bits (Half Precision) Floating Point Calculation


Pix taken from Comparison of NVIDIA Tesla/Quadro and NVIDIA GeForce GPUs

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Compiling OpenFOAM-5.0 with Intel-MPI

Minimum Requirements version

  1. gcc: 4.8.5
  2. cmake: 3.3 (required for ParaView and CGAL build)
  3. boost: 1.48 (required for CGAL build)
  4. fftw: 3.3.7 (optional – required for FFT-related functionality)
  5. Qt: 4.8 (optional – required for ParaView build)

I’m using Intel-16.0.4 and Intel-MPI-5.1.3.258

Step 1a: Download and Unpacking Sources

# wget -O - http://dl.openfoam.org/source/5-0 | tar xvz
# wget -O - http://dl.openfoam.org/third-party/5-0 | tar xvz

Step 1b:  Rename the Directory

# mv OpenFOAM-5.x-version-5.0 OpenFOAM-5.0
# mv ThirdParty-5.x-version-5.0 ThirdParty-5.0

Step 2: Initiate Intel and Intel-MPI Environment and source OpenFOAM-5.0 bashrc

source /usr/local/intel/bin/compilervars.sh intel64
source /usr/local/intel/parallel_studio_xe_2016.4.072/bin/psxevars.sh intel64
source /usr/local/intel/impi/5.1.3.258/bin64/mpivars.sh intel64
source /usr/local/intel/mkl/bin/mklvars.sh intel64
source /usr/local/OpenFOAM/OpenFOAM-5.0/etc/bashrc
export MPI_ROOT=/usr/local/intel/impi/5.1.3.258/intel64

Step 3: Make sure your CentOS-7 Environment have the following base packages

# yum install gcc-c++ gcc-gfortran gmp flex flex-devel boost zlib zlib-devel qt4 qt4-devel

Step 4: Edit the OpenFOAM  internal bashrc

# vim /usr/local/OpenFOAM/OpenFOAM-5.0/etc/bashrc

Line 35,36

export WM_PROJECT=OpenFOAM
export WM_PROJECT_VERSION=5.0

Line 45

FOAM_INST_DIR=/usr/local/$WM_PROJECT

Line 60

export WM_COMPILER_TYPE=system

Line 65

export WM_COMPILER=Icc

Line 88

export WM_MPLIB=INTELMPI

Step 5: Compile OpenFOAM

# ./Allwmake -update -j
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Faulty disks accepting I/O request and not returning any failure for GPFS

We have encountered a situation where a defunct disk was accepting IO request and did not return any failure in time. As a result, these IO requests hanged there till time out (default 10 seconds). Typically, Spectrum Scale/GPFS will fail to read or write a disk, the failure is written in log and we have to shift IO to other available disks which should be quick.

Normally such operations should return in 20 milliseconds or less. When we have IO timeout, this request has wasted us
10 seconds / 20 milliseconds = 500 times of time. Even if Spectrum Scale/GPFS is able to choose a fast disk in the second attempt, we are much slower than normal.

Due to the utilization of striping technology, a bad/slow disks always affects IO of many files, much more than the situation without striping. IO on the same file involves more than several disks, and the IO has to wait for the slowest request to return. So a bad/slow disk may have considerable influence on Spectrum Scale/GPFS performance.

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“The command gnome-session existed with signal 15” on CentOS 7 for FastX2

If you have an error message when you launched FastX2 client, you will see this error “The command gnome-session existed with signal 15” on CentOS 7 for FastX2.

Step 1: This error is caused by selinux on CentOS 7. Do the following /etc/selinux

SELINUX=disabled

Trying to use the command “setenforce 0” does not seems to be able to fix the issue.

Step 2: Remember to install GNOME Desktop

# yum groupinstall "GNOME Desktop" "Graphical Administration Tools"

Step 3: Uninstall the StarNetFastX2 and reinstall

# rpm -e StarNetFastX2
# rpm -Uvh --force StarNetFastX2-2.4.7.rhel6.x86_64.rpm