System FAQs
Cannot start license on Linux - my network adapter doesn't start with eth
This article pertains to the user ensuring the correct license and the support libraries have been installed. The version of FlexNet we ship our software with relies on the network adapter to have the prefix of eth. If your network adapter is not eth0, eth1, etc, then you will need to update your version of the license daemon.
Examples of network adapters that need the updated daemon are "em1" and "p7p1". You can see your network configuration with "ifconfig -a". In order to update the license daemon, please change to the license folder in the application directory, make a folder called "old" and move "lm*" and "geotomo" into this folder. You will then download and extract the contents of this archive into the license folder and run "tar xvf flexnet64_11.12.1.tar". If you get "permission denied" running any of the commands, ensure you run them as the user that owns the folder/files or run it as root.
Please note that version 11.12.1 will not support the FlexNet version 9 of the license dongles.
Published on 19-NOV-2017
FAQ ID #172
How can I change my resolution to 1080p in Hyper-V to display the software correctly?
You will login to the system, open a terminal, and su to root. Then run the command
grubby --update-kernel=ALL --args="video=hyperv_fb:1920x1080
Published on 6-DEC-2020
FAQ ID #224
How do I get a license?
If you have already downloaded the software package and need a license, you will need to download the appropriate script for your operating system and run the script. Once you have run the script, a text file is generated in the folder you ran the script. You will need to send us this text file and we will create and send a license.
Download the script for
Windows
Linux
Published on 19-NOV-2017
FAQ ID #174
"ssh connect to host port 22: Connection refused"
Please ensure you can ssh to the machine from a terminal. This error message is usually indicative that the service is either not installed and/or running.
You may need to have someone with root access to run "/etc/init.d/sshd restart" or "service sshd restart".
Published 18-OCT-2017
FAQ ID #129
Cannot start license on Linux - my workstation is not connected to a network
The licenses we send are network-enabled licenses, which pose an issue with stand-alone workstations that are not connected to a network. If you attempt to start the license and your machine and receive an error message from the GUI like "operation in progress" or "cannot contact license server", first verify the actual error. You may do this with running "(APPLICATION_PATH)/license/lmdown", and manually trying to start the license with "lmgrd -c (license_file).lic". If it complains about not being able to find or resolve the host in the license (usually will say "license specifies THIS_NAME, but host reports the hostname is SOMETHING_ELSE", please follow the below steps:
1. If you run "ifconfig" and there is no "eth0" or "em0" or "p7p1" adapters, but it shows up when running "ifconfig -a", you will need to type "hostname" and then edit /etc/hosts to include "(hostname) 192.168.1.2". Verify this hostname is on the first line of the license file. Make sure the network adapter is disconnected, then run "ifconfig eth0 192.168.1.2 up". You should be able to run "ping -c 1 (hostname)" and get a response from your local machine. Bring down ("lmdown") the license and try to manually start it again.If you have manually brought up the network adapter and will place it on a network, you must make sure the IP address does not conflict with other devices on the network.
2. You may edit the hostname of the license file. Anything else will cause the license to become invalid. Try modifying the license file's hostname to "localhost". The location for the hostname is in the first line of the license file. The format is "SERVER (hostname) (hardware address of network adapter/disk serial number/dongle address". The hostname "localhost" means "this machine" in layman's terms. The name "localhost" is also what you will use in the machine list when you start processing data / running projects.
Published on 20-NOV-2017
FAQ ID #175
Required Libraries
If you use an alternative shell or a distribution other than CentOS 5.x series you may have to install some libraries for compatibility. Please refer to your system documentation on the correct installation procedures, just to make sure.
CentOS 4 & 5 / RHEL 4 & 5
· yum install xterm libXext numactl libnuma1 compat-f2c redhat-lsb
CentOS 6 & 7 / RHEL 6 & 7
· yum install xterm libXext numactl redhat-lsb compat-libgfortran-41
CentOS 8 / RHEL 8
· yum install epel-release
· yum install lsb libnsl xterm libXext numactl compat-libgfortran-48
Ubuntu 10 and higher
· apt-get install lsb-core numactl libf2c2 libnuma1 xterm
*** Earlier versions of Ubuntu will require you to install gcc-3.4 libs and correctly install libg2c0 for your distribution ***
*** CentOS/RHEL 4 will require a different version of libnuma.so than included in the package. Please contact support@geotomo.com for assistance receiving this patch ***
Published on 17-NOV-2017
FAQ ID #171
I am running the Linux software through a Windows X11 emulator and having display problems
Traditionally we do not run our Linux software through X11 on Windows. We have found that certain Windows X11 window managers have problems displaying certain graphics elements of the software, including tabs, cursors, 2D/3D models, etc.
These problems arise when you may be using XMing for Windows. Please try to download and use Moba and make sure you are using “ssh –X” from the shell provided when you launch Moba.
Published 18-OCT-2017
FAQ ID #138
How do I run a stand-alone license server?
If you would like to run your own license server, you may download one of the following archives:
Windows Version 11.10.1 [comes with current packages - supports green dongle version 9]
Linux Version 11.10.1 - supports version 9 of the dongle, network adapter must be named eth [supports green dongle version 9 - daemon being replaced with 11.16.5.1 do to a vulnerability. you can replace the file if it's not included in your package.]
Linux Version 11.12.1 - does not support version 9 of the dongle, only 10, supports network adapters named something other than eth
Linux Version 11.13.1 - use this version if the vendor daemon constantly restarts when trying to run "lmgrd" - it fixes some timing issues
Linux Version 11.16.5.1 - latest version that included the HEARTBEAT FIX where certain code could cause the vendor/license deamons to stop talking to each other, not allowing license feature checkouts or checkins, and a service restart would be required. [We plan on including this package in future software releases.]
Linux Version 11.17.1.0 - contains security fixes and support for virtual machines. extract, run "./publisher/install_fnp.sh && ./lmutil hostid -ptype VM -uuid". we will make the license with the VM_UUID.
You will extract the contents of the archive to a folder, place the license in the folder, and go to a command line to setup the stand-alone server:
For Linux, you run "/path/to/lmgrd -c /path/to/license/(filename.lic) -l /path/to/lmgrd.log" [To survive a server reboot, we recommend putting it in /etc/rc.local].
For Windows, you run "c:\path\to\lmgrd.exe -z -c (filename.lic) -lc:\path\to\lmgrd.log". Once you have brought the server online, you have the option of copying the license file into the license folder of the application (the license service will read it and find your stand-alone server).
For Linux workstations, you can also create ~/.flexlmrc and put the text "GEOTOMO_LICENSE_FILE=27000@server" (where server is the name of the license server). The 27000 number is the default port number, which can be customized by modifying the license file and putting a number after the hardware address of the network adapter or the license dongle identifier. You must make sure no other application uses this number.
Most admins will either create a non-privileged user and create a .bat file to run it on startup or they will use the lmtool.exe binary (in Windows) to create an auto-start service. If it's a stand-alone server, then we recommend any of the above. Windows license daemons can run some of our newer Linux software and vice-versa.
To then check the status, you would run "./lmstat -c (filename.lic)" [Linux] or "lmstat -c (filename.lic)" [Windows].
There are many options when running a stand-alone server, so please contact support for more information.
Published 19-NOV-2017 / Latest Revision 20-AUG-2020
FAQ ID #173
Gathering system information on non-English system
GeoTomo generates licenses based on information sent back from the gather_info.bat script. Sometimes the script is run on systems that do not have the English codepage set. The system administrator can set the operating system's language to English, but this is time-consuming and tedious for many reasons. There is a solution that is capable of changing the codepage temporarily and back via two seperate .bat scripts.
You can download the script from here. After extracting the contents, please run "englishize.bat" and then our system gather script and send back the results. You can restore your language's codepage by running "restore.bat".
The script to change the codepage and more information is from Microsoft, located at this link.
Published 14-DEC-2018
FAQ ID #213
MY WORKSTATION IS NOT CONNECTED TO A NETWORK (LINUX ONLY).
The licenses we send are network-enabled licenses, which pose an issue with stand-alone workstations that are not connected to a network. If you attempt to start the license and your machine and receive an error message from the GUI like "operation in progress" or "cannot contact license server", first verify the actual error. You may do this with running "(APPLICATION_PATH)/license/lmdown", and manually trying to start the license with "lmgrd -c (license_file).lic". If it complains about not being able to find or resolve the host in the license (usually will say "license specifies THIS_NAME, but host reports the hostname is SOMETHING_ELSE", please follow the below steps:
1. If you run "ifconfig" and there is no "eth0" or "em0" or "p7p1" adapters, but it shows up when running "ifconfig -a", you will need to type "hostname" and then edit /etc/hosts to include "(hostname) 192.168.1.2". Verify this hostname is on the first line of the license file. Make sure the network adapter is disconnected, then run "ifconfig eth0 192.168.1.2 up". You should be able to run "ping -c 1 (hostname)" and get a response from your local machine. Bring down ("lmdown") the license and try to manually start it again.If you have manually brought up the network adapter and will place it on a network, you must make sure the IP address does not conflict with other devices on the network.
2. You may edit the hostname of the license file. Anything else will cause the license to become invalid. Try modifying the license file's hostname to "localhost". The location for the hostname is in the first line of the license file. The format is "SERVER (hostname) (hardware address of network adapter/disk serial number/dongle address". The hostname "localhost" means "this machine" in layman's terms. The name "localhost" is also what you will use in the machine list when you start processing data / running projects.
If you have any problems or questions with this, please contact us for assistance.
Published 1-APR-2019
FAQ ID #100
SETUP OF PASSWORDLESS SSH
After the new user can successfully login to their machine, you will need to make sure they have access to the machine and ports for the license server.
Quick-Start: Login as that user and open a terminal in X-Windows and run:
ssh-keygen -t dsa
cd ~/.ssh
cat id_dsa.pub >> authorized_keys
cat id_dsa.pub >> authorized_keys2 **
chmod 600 ~/.ssh/auth*
This sets up the keys, permissions, and verifies ssh to each node without a password (which is very important to deploy jobs). After that you should be able to “ssh localhost” and verify they don’t need a password. If you are unable to do so, please double check your steps and retry. Also make sure the ssh service is running (“/etc/init.d/sshd start” or “/etc/init.d/openssh-server start”) and you have correct permissions on the files in “~/.ssh”.
** This is dependent on your current setup. Please check your system configuration and select the appropriate choice or check with the systems administrator.
Published 1-APR-2019
FAQ ID #102
3DVIEWM MODULE NOT RUNNING OVER VNC/NXCLIENT (LINUX ONLY)?
Please make sure the latest video drivers, X11 drivers, Linux distribution updates (including mesa-utils and any open source drivers you use [if you don’t use manufacturer drivers]), and user profile have been installed and updated correctly. If the machine running VNC you must connect to display :0 to render the graphics or you will get a blank screen.
You may also try to force indirect and software rendering (depending on your shell):
export LIBGL_ALWAYS_INDIRECT=1
export LIBGL_ALWAYS_SOFTWARE=1
** If you have an NVidia card these LIBGL flags will have no effect.
In Linux, the method for 3DViewM to work is:
GPU in the machine -> ssh –X (machine with GPU)
No GPU in the machine -> ssh –X (machine without GPU)
GPU in the machine -> ssh –X (machine without GPU) will not work correctly
Published 1-APR-2019
FAQ ID #104
FLEXNET LICENSE DAEMON: SYSTEM TIME ERROR – 88?
If the computer’s clock gets changed after the daemon has been run, you’ll encounter this message – it is a license protection scheme. You’ll want to check the time on the nodes you’re trying to run the software on and the computer the license server is running on. Please contact GeoTomo’s support if you cannot remove this message by rebooting and restarting the daemon.
FAQ ID #106
CentOS 5.7 & 5.8
CentOS 5.7 & 5.8 have compatibility/shared lib issues so if you can install a different version, please do so to avoid potential conflicts. This doesn’t affect RedHat Enterprise Linux 5 though.
FAQ ID #107
Cannot access my NFS shares from my Redhat-based kernel.
There is a known bug in kernel 2.6.9 and was fixed in 2.6.18 with the way it tries to access NFS shares on other machines. You might try NFS with –o noatime,nodiratime,vers=3,proto=tcp but it’s not guaranteed to work with all combinations of Linux distributions. With our computing nodes we run CentOS 5.5, but utilize Ubuntu 10.04LTS on data, home, and NIS server.
FAQ ID #108
My cluster keeps losing connection to my NFS host.
If you get system “pauses” while cd or ls an NFS directory and the /var/log/messages reports something about a timeout while access the hostname of the NFS server, this will require a little tweaking of your NFS server. If you have over 50 computers that will initiate an NFS mount to the same machine, you’ll need to have more than the system’s default 8 concurrent NFSd instances running as well as adequate bandwidth in your network.
FAQ ID #109
My NFS mount command keeps returning permission denied.
First make sure you’re allowed in the /etc/exports, the gid/uid settings of the mount, the nfs daemon is running on the machine, and that either portmap and/or other related daemons are allowed access in /etc/hosts.allow. If you continue to get permission denied, check your kernel version, and that /proc/sys/nfsd exists. If not, run “mount –t nfsd nodev /proc/sys/nfsd” on debian/Ubuntu or on redhat-based kernels you should check for “proc/fs/nfsd” and run “mount –t nfsd nodev/proc/fs/nfsd”. Also note that by default, nfs uses the option of root_squash, to disallow the root user of any machine to write to those shares, a way to prevent anyone from doing things as root where they aren’t supposed to. Please make sure the appropriate person in the IT department is performing the troubleshooting, as there might be other underlying issues.
FAQ ID #110
MPI job hangs or isn’t running properly.
There can be a number of reasons why your job may not run correctly. After verifying the mounts and you’ve made sure there are no system problems, the next step to try is editing the runtime script generated (usually created in the data folder of the project and includes the word “_runScript”) and placing following text after “mpirun” but before “-np”:
--mca btl_base_verbose 30 –-mca plm_base_verbose 100
This will increase the verbosity of mpirun and include information that will assist in troubleshooting in the job’s log file. Please send the log file, screen shots, and any relative information to support when contacting us about the issue.
Published 1-APR-2019
FAQ ID #111
Linux keeps showing very little to no free physical memory and I have plenty.
Most of the time the kernel will cache files and keep them resident for a certain amount of time, but sometimes doesn’t release the cache. A safe method to flush the cache is to run “echo 3 > /proc/sys/vm/drop_caches” and then "sync", which writes all data to disk and then flushes it. Please note that the next time you access a large file, the kernel will cache it again, and it may take longer than before the cache was flushed. Check your documentation on assistance with changing the mbcache modules and settings. You may also want to tune /etc/sysctl.conf and the vm.swappiness setting. We try to utilize 10 on an SSD based high memory cluster machine.
FAQ ID #112
I get the error “Could not create the Java virtual machine”.
Follow these steps:
- Verify there is enough free space on the drive (df –h)
- Verify memory reserves / Clean up running processes
- Change the option “MaximumHeapSize” in ~/.geotomo/config.xml to a lower number and restart the launcher
FAQ ID #113
I get the error “Could not load background” when trying to start the software.Make sure you have space available in /tmp (or whichever folder the TMP and/or TMPDIR export points to). By default, the system should use /tmp but the systems administrator can change this.
FAQ ID #114
libg2c.so not found
This library is required to run some of the Fortran code in our software. You will need to search for the RPM if you use RHEL/CentOS/SuSE and install it (as root) with "rpm -i (rpmname).rpm".
For Debian/Ubuntu, please search online for the package "libg2c0_3.4.6-8ubuntu2_amd64.deb" and use the command "dpkg -i --force-all libg2c0_3.4.6-8ubuntu2_amd64.deb" to install it.
To find the RPM for your specific distribution, please visit http://rpm.pbone.net and search for "libg2c.so".
Version 10 and below of Ubuntu, you can find the package in the repository as "libf2c2" and install it with the command: "apt-get install libf2c2".
Published 1-APR-2019
FAQ ID #115