Month: May 2020

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xRDP Connection Errors on CentOS 6

After yum install xrdp and starting the service, I encountered the error during remote desktop to the Linux Box.

connecting to sesman ip 127.0.0.1 port 3350
sesman connect ok
sending login info to session manager, please wait...
xrdp_mm_process_login_reponse: login successful for display
started connecting
connecting to 127.0.0.1 5910
error - problem connecting

At the /var/log/xrdp-sesman.log

......
[20141118-23:53:40] [ERROR] X server for display 10 startup timeout
[20141118-23:53:40] [INFO ] starting xrdp-sessvc - xpid=2998 - wmpid=2997
[20141118-23:53:40] [ERROR] X server for display 10 startup timeout
[20141118-23:53:40] [ERROR] another Xserver is already active on display 10
[20141118-23:53:40] [DEBUG] aborting connection...
[20141118-23:53:40] [INFO ] ++ terminated session:  username root, display :10.0
.....

I have installed the necessary GNOME Desktop packages. Installing GNOME Desktop on CentOS 6 on a console before installing xrdp.

But the solution is quite simple. You need to install the tigervnc-server package and just the tigervnc only.

# yum install tigervnc-server

Restart the xrdp again.

# service xrdp restart

 

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Trying to allocate 1005 pages for VMLINUZ error when booting with RHEL or CentOS 6.5 disks

VMLINUZ2

I was booting the RHEL 6.5 or CentOS 6.5 on a IBM PureFlex System and I have this error. This occurs when When installing Red Hat Enterprise Linux 6 from DVD media the installation will default to native Extensible Firmware Interface (EFI) mode boot. I do not have

According to IBM Website,

The workaround is simply to install the operating system in the traditional legacy mode, since there is generally no reason to install in other than Legacy mode. The workaround is only necessary if the media you are booting defaults to EFI mode (DVD or EFI Preboot eXecution Environment (PXE)) otherwise a legacy installation (e.g. – traditional PXE) is the default and is unaffected by this issue.

To force a legacy installation of the operating system from the EFI bootable DVD media the user should:

Press F12 key when the IBM splash screen is shown during system boot.
Select Legacy Only option and press Enter.
The operating system will boot and install in traditional legacy boot mode.

And the issue was resolved.

References:

  1. Red Hat Enterprise Linux 6 (RHEL6) native Extensible Firmware Interface (EFI) install is not supported with greater than 512 GB memory – IBM System x and BladeCenter
  2. Bug 691860 – UEFI version of ISO fails to boot when >4gig (since f14)
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Limiting Users on PBS Professional

Scenario 1: How do we restrict the users to a certain maximum job size within a maximum concurrent number of jobs?

For example, if you would like to restrict users using this queue to a maximum of 4 cores per jobs. But his or her concurrent jobs cannot exceed 16?

qmgr -c "set queue workq max_run_res.ncpus = [u:PBS_GENERIC=16]"
qmgr -c "set queue workq resources_max.ncpus = 4"

The first limit sets max of 16 cores per user for the workq queue (for all jobs)
The second limit sets max of 4 cores per job for workq queue

Scenario 2: How do we ensure that users only run a minimum number of cores in the queue?

For example, if you would like to restrict the users to a minimum 32 cores per job.

qmgr -c " s q workq resources_min.ncpus=32"

Test:

qsub -l select=1:ncpus=16 -q workq -- /bin/sleep 100
qsub: Job violates queue and/or server resource limits

Scenario 3: How do we ensure that users run a minimum number of GPGPU in the queues?

qmgr -c "set server max_run_res.ngpus = [p:my_project_code=2]"

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Opening the Door to Big Memory

Join MemVerge, IDC, Intel, NetApp, and Penguin Computing in a webcast introducing a new category of IT that turns scarcity into abundance.

Tuesday, May 19th at 9:00 AM PST

This Webcast Introduces a New Wave of Computing: Big Memory Computing

Memory has been a wonderfully fast but scarce computing resource. This scarcity has resulted in major constraints that prevent applications from processing large amount of real-time data effectively.

These constraints are being removed by a new way of computing: Big Memory Computing. Today, the confluence of persistent memory and Big Memory software makes memory abundant, persistent and highly available. Together, they promise to make the IT world stop, think, and change the way applications are developed and deployed………

For more information, see https://www.memverge.com/opening-the-door-to-big-memory/

To register see https://us02web.zoom.us/webinar/register/WN_gDXc3wD7QtaLhMNc8PCQPg

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How is the nproc hard limit calculated and how do we change the value on CentOS 7

Sometimes, you may encountered errors like this during an intensive run.

How do you know the value of the hard limit set? There is a good article by RedHat that explained “How is the nproc hard limit is calculated”

According to the article,

The limit depends on the total memory available on the server, which is calculated at boot time by the kernel as explained below:

/*
* Resource limit IDs
*
* ( Compatibility detail: there are architectures that have
* a different rlimit ID order in the 5-9 range and want
* to keep that order for binary compatibility. The reasons
* are historic and all new rlimits are identical across all
* arches. If an arch has such special order for some rlimits
* then it defines them prior including asm-generic/resource.h. )
*/

#define RLIMIT_CPU 0 /* CPU time in sec */
#define RLIMIT_FSIZE 1 /* Maximum filesize */
#define RLIMIT_DATA 2 /* max data size */
#define RLIMIT_STACK 3 /* max stack size */
#define RLIMIT_CORE 4 /* max core file size */

#ifndef RLIMIT_RSS
# define RLIMIT_RSS 5 /* max resident set size */
#endif

#ifndef RLIMIT_NPROC
# define RLIMIT_NPROC 6 /* max number of processes */
#endif

#ifndef RLIMIT_NOFILE
# define RLIMIT_NOFILE 7 /* max number of open files */
#endif

#ifndef RLIMIT_MEMLOCK
# define RLIMIT_MEMLOCK 8 /* max locked-in-memory address space */
#endif

#ifndef RLIMIT_AS
# define RLIMIT_AS 9 /* address space limit */
#endif

#define RLIMIT_LOCKS 10 /* maximum file locks held */
#define RLIMIT_SIGPENDING 11 /* max number of pending signals */
#define RLIMIT_MSGQUEUE 12 /* maximum bytes in POSIX mqueues */
#define RLIMIT_NICE 13 /* max nice prio allowed to raise to
0-39 for nice level 19 .. -20 */
#define RLIMIT_RTPRIO 14 /* maximum realtime priority */
#define RLIMIT_RTTIME 15 /* timeout for RT tasks in us */
#define RLIM_NLIMITS 16
8<---------- 8< ---------------- 8< ---------------- 8< --------

According to the article, For nproc, the limit is calculated in the kernel before the first process is forked in kernel/fork.c called by start_kernel:

>> init_task.signal->rlim[RLIMIT_NPROC].rlim_cur = max_threads/2;
>> init_task.signal->rlim[RLIMIT_NPROC].rlim_max = max_threads/2;

Below is the path to the function :

>> start_kernel
> fork_init(totalram_pages)
> if (max_threads < 20) max_threads = 20;
> init_task.signal->rlim[RLIMIT_NPROC].rlim_cur = max_threads/2;
> init_task.signal->rlim[RLIMIT_NPROC].rlim_max = max_threads/2;

>>>> RLIMIT_NPROC = max_threads/2

- The value of these variables are:

-> max_threads = mempages / (8 * THREAD_SIZE / PAGE_SIZE);
mempages comes from the function argument : fork_init(totalram_pages);
-> #define THREAD_ORDER 2
-> #define THREAD_SIZE (PAGE_SIZE << THREAD_ORDER)
-> PAGE_SIZE = 4096 (but useless)

- mempages is assigned in dmesg during the boot process, for example:

>> Memory: 36 989 916k/38797312k available (5516k kernel code, 1049156k absent, 758240k reserved, 6912k data, 1332k init)
mempages = 36989916k / PAGE_SIZE = 36989916k / 4096 = 9 247 479

- As an example:

RLIMIT_NPROC = (mempages / (8 * THREAD_SIZE / PAGE_SIZE)) / 2
= (mempages / (8 * (PAGE_SIZE << THREAD_ORDER) / PAGE_SIZE )) /2
= ( 9247479 / (8 * (4096 * 4) / 4096 )) / 2
= ( 9247479 / (8 * 4 )) /2
RLIMIT_NPROC = 14 4491.859375

To look at the values of the hard limits using BASH, you can use the command

ulimit -hn
4096

To modify the limits, do proceed to /etc/security/limits.d/20-nproc.conf to change the number

# Default limit for number of user's processes to prevent
# accidental fork bombs.
# See rhbz #432903 for reasoning.

* soft nproc 4096
root soft nproc unlimited

 

References:

  1. How is the nproc hard limit calculated?
  2. How to set nproc (Hard and Soft) Values in CentOS / RHEL 5,6,7
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Compiling ScaLAPACK-2.0.2 on CentOS 7

Prerequisites for SCALAPACK:

  1. Building BLAS Library using Intel and GNU Compiler
  2. Building LAPACK 3.4 with Intel and GNU Compiler
  3. OpenMPI-3.1.4
  4. GNU-6.5

To compile the SCALAPACK

mkdir -p ~/src
wget http://www.netlib.org/scalapack/scalapack-2.0.2.tgz
tar -zxvf scalapack-2.0.2.tgz
cd scalapack-2.0.2
cp SLmake.inc.example SLmake.inc

Edit the scalapack SLmake.inc file. At line 58 and line 59

BLASLIB       = -lblas -L/usr/local/blas
LAPACKLIB     = -llapack -L/usr/local/lapack/lib

At the Linux Console again

make
mv scalapack-2.0.2 /usr/local/

Update and export your LD_LIBRARY_PATH

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Setup of Linux OneDrive on CentOS 7

Introduction:
Sometime, you have a huge data sets to transfer and you may not want to hold an active connection all the time. One solution is to use OneDrive especially if you or your organisation has subscribed to Office 365. You should have 1TB of online space.

Step 1: Install Dependencies

yum install libcurl-devel
yum install sqlite-devel
curl -fsS https://dlang.org/install.sh | bash -s dmd
yum install libnotify-devel

Step 2: Git Clone the OneDrive Code

git clone https://github.com/abraunegg/onedrive.git
cd onedrive
./configure
make clean
make
sudo make install

Step 3a: Authorize Microsoft to access your account

You need to authorize onedrive with Microsoft so it can access your account. First start by typing on the console

onedrive

Step 3b: You will be prompted to visit the URL to get permission

Step 4: Log in to your OneDrive account, and grant the app permission to access your account

Step 5: You will see a blank white page. Copy the URL and paste it into the Xterm

Step 6: Copy the URL and paste it into the Xterm  “Enter the response uri”

 Configuration

By default, all files are downloaded in ~/OneDrive and hidden files are skipped.  If you want to change the defaults, you can copy and edit the included config file into your ~/.config/onedrive directory:

mkdir -p ~/.config/onedrive
cp /usr/local/onedrive/config ~/.config/onedrive/config
vim ~/.config/onedrive/config

Available options:

  • sync_dir: directory where the files will be synced
  • skip_file: any files or directories that match this pattern will be skipped during sync.

For example,

If I want to sync everything except Confidential and Personal Folders

# Directory where the files will be synced
sync_dir = "~/OneDrive/"
# Skip files and directories that match this pattern
skip_file = ".*|Confidential|Personal"

Note: after changing the sync list, you must perform a full synchronization by executing

onedrive --resync --synchronize

Step 7: Sync List

If you wish to do selective sync instead of the whole OneDrive Folder, you can create a file called sync list and put it in the “~/.config/onedrive” folder and add the relative path from the OneDrive to the folder you want to sync 

% touch ~/.config/onedrive/sync_list

For example, when you place a g2o folder into ~/OneDrive and only one to sync this particular folder. Your sync_list should only contain 

g2o

One Drive Service

If you want to sync your files automatically, enable and start the systemd service:

systemctl --user enable onedrive
systemctl --user start onedrive

References:

  1. How to Sync Microsoft OneDrive with Linux
  2. https://github.com/abraunegg/onedrive

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Installing DiffBind for R-3.6.2

To Install DiffBind, you can follow the instruction found at DiffBind

First thing first, you would need to install BiocManager and then install DiffBand

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DiffBind")

At the end, you should get

To view Documentation,

browseVignettes("DiffBind")