SAMSON with hybrid graphics cards (Intel/Nvidia)

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Wed, 15 May 2019 13:18:57 GMT

DmitriyMarin — Wed, 15 May 2019 13:18:57 GMT

Dear @Ivan ,
Thanks to issues raised on the forum, we have fixed the issue in SAMSON causing problems with the viewport when using Intel integrated graphics processor. This issue might have been causing the problem you have posted in this thread. The new installation of SAMSON should resolve the issue.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 26 Apr 2019 06:41:11 GMT

Ivan — Fri, 26 Apr 2019 06:41:11 GMT

@dmitriymarin said in SAMSON with hybrid graphics cards (Intel/Nvidia):

@ivan
Yes, sorry, it can consume quite a lot sometimes. For me, for example, just the interface consumes sometimes 30-50% of one CPU core. To decrease the CPU consumption, you can hide the Document view (Ctrl/Cmd+1) or the Inspector (Ctrl/Cmd+I) when you do not need them. There is an issue with them which causes such consumption. It will be fixed in the next version of SAMSON.

Will wait :) SAMSON has very cute interface, however such cost of one core for that it is not acceptable!

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 26 Apr 2019 02:48:07 GMT

Ivan — Fri, 26 Apr 2019 02:48:07 GMT

@dmitriymarin Now I am using Nvidia PRIME like you showed in screenshot above. I do not think, that it is driver issue, but it is how you utilize them. I am also developing some software with OpenGL, however by using lower version API (1.2). So it works both Intel and Nvidia cards. I think, that advanced functions like in OpenGL 3.2 should be used using procedure addresses like it is doing with SDL_GL_GetProcAddress.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Thu, 25 Apr 2019 20:56:31 GMT

DmitriyMarin — Thu, 25 Apr 2019 20:56:31 GMT

@ivan
Yes, sorry, it can consume quite a lot sometimes. For me, for example, just the interface consumes sometimes 30-50% of one CPU core. To decrease the CPU consumption, you can hide the Document view (Ctrl/Cmd+1) or the Inspector (Ctrl/Cmd+I) when you do not need them. There is an issue with them which causes such consumption. It will be fixed in the next version of SAMSON.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Thu, 25 Apr 2019 20:48:53 GMT

DmitriyMarin — Thu, 25 Apr 2019 20:48:53 GMT

@Ivan
Great! I am glad that you solved the issue! Apparently, it was a problem with drivers. Do you use primusrun/optirun or just nvidia GPU directly?

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Thu, 25 Apr 2019 20:47:14 GMT

Ivan — Thu, 25 Apr 2019 20:47:14 GMT

Should interface eat so much 96% CPU from one of cores ?

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Thu, 25 Apr 2019 20:38:50 GMT

Ivan — Thu, 25 Apr 2019 20:38:50 GMT

I installed Linux Mint 19.1 and installed nvidia-driver-390. Now interface has no such troubles. Thank you for advices.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Sat, 02 Mar 2019 16:20:23 GMT

DmitriyMarin — Sat, 02 Mar 2019 16:20:23 GMT

@ivan said in SAMSON with hybrid graphics cards (Intel/Nvidia):

I tried, and that did not help.

Apparently, SAMSON might be having a problem properly detecting your GPU during the installation, even with primusrun.

Nvidia PRIME does not go with Bumblebee/optirun/primusrun, it is an Nvidia technology and it also allows one to switch between CPU and Nvidia GPU without additional layers giving a direct OpenGL access, which is more preferable. It is done via GPU offloading. But it comes with a downside: for a switch between CPU and GPU to take an effect one needs to log out and log in back (OS needs to do some re-initializations).

You can check whether you have Nvidia PRIME or not in the Nvidia X Server Settings. Nvidia PRIME is either installed together with an nvidia proprietary driver or you can install it via (after installing nvidia proprietary drivers):

sudo apt install nvidia-prime

Note: To use Nvidia PRIME you might need to remove Bumblebee/optirun/primusrun.

Note: In case, if you are using Nvidia PRIME, SAMSON should be installed with an active Nvidia GPU and to use SAMSON it would be necessary to enable to Nvidia GPU.

Personally, on my laptop with Ubuntu 16.04 and equipped with Nvidia GeForce GTX 670MX I have the nvidia-384 driver installed with Nvidia PRIME. I had Bumblebee installed many years ago, but I could not make it work with CUDA.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Sat, 02 Mar 2019 06:22:35 GMT

Ivan — Sat, 02 Mar 2019 06:22:35 GMT

@dmitriymarin said in SAMSON with hybrid graphics cards (Intel/Nvidia):

Have you tried to install SAMSON with primusrun and then launching SAMSON with it?

I tried, and that did not help.

If there is a configuration file for optirun/primusrun which allows specifying which apps should use GPU you may try specifying GPU for SAMSON.

There is no such a file :( It is controlled by the prefix in the command line when I calling the app.

Is it possible for you to try with nvidia-prime? It should provide better OpenGL support compared to optirun since optirun has an additional layer VirtualGL which might be causing this issue.

I have no such a command nvidia-prime... If I understand correct, primusrun have no such an extra layer.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 15:47:05 GMT

DmitriyMarin — Fri, 01 Mar 2019 15:47:05 GMT

Have you tried to install SAMSON with primusrun and then launching SAMSON with it?

If there is a configuration file for optirun/primusrun which allows specifying which apps should use GPU you may try specifying GPU for SAMSON.

Is it possible for you to try with nvidia-prime? It should provide better OpenGL support compared to optirun since optirun has an additional layer VirtualGL which might be causing this issue.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 15:33:00 GMT

DmitriyMarin — Fri, 01 Mar 2019 15:33:00 GMT

Python is not used by SAMSON, Python is present in the launching script just to add a path to its libraries so that users could use the Python Scripting Element. So you can safely comment the Python-related block in the launching script if you are not using the Python Scripting Element.

The information you see in the About dialogue (or in Preferences > Installation > General) shows all the graphics cards, meaning that it can show both CPU and GPU. But in your case, the SAMSON installer could not find your Nvidia GPU.

Personally, I used SAMSON before on a laptop with Linux (Ubuntu) equipped with Nvidia GeForge GTX 670MX GPU (which has Optimus technology) but without Bumblebee/optirun installed. So the problem seems to be either in SAMSON not being able to properly detect GPU or lack of some drivers.

How did you install SAMSON? With optirun or without? Does it give you the same behavior in both cases?

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 15:29:58 GMT

Ivan — Fri, 01 Mar 2019 15:29:58 GMT

@dmitriymarin

Do you have the Nouveau driver blacklisted or uninstalled? Because it causes some issues on Nvidia Optimus GPUs.

Yes.

dia@lenovo:~$ cat /etc/modprobe.d/nvidia-blacklists-nouveau.conf
# You need to run "update-initramfs -u" after editing this file.

# see #580894
blacklist nouveau

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 15:10:40 GMT

Ivan — Fri, 01 Mar 2019 15:10:40 GMT

It is really strange, that even if I tried to run it with optirun or primusrun in about dialog it showing, that I still using Intel HD card.

I think there is some hidden restart of application GUI inside some python stuff, so really it does not use Nvidia card at all.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 11:45:27 GMT

DmitriyMarin — Fri, 01 Mar 2019 11:45:27 GMT

Actually, you should not worry about the following libpng warning:

libpng warning: iCCP: known incorrect sRGB profile

The libpng warning might be caused by libpng provided with your Python installation. To check whether this causes the problem, you could try commenting the addition of a path to Python libraries in the SAMSON-Core.sh script:

#export LD_LIBRARY_PATH=${PYTHON_LIBRARY_PATH}:${LD_LIBRARY_PATH}

I do not think that it is due to libpng, rather it might be a problem of a driver and OpenGL layer provided by Bumblebee.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 11:35:14 GMT

Ivan — Fri, 01 Mar 2019 11:35:14 GMT

It warns about libpng version. I think, that can be the reason. Which version of libpng is required?

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 11:33:11 GMT

Ivan — Fri, 01 Mar 2019 11:33:11 GMT

optirun glxgears works fine, I am intensively using VMD software with Nvidia. primusrun also runs well.

I add --logconsole flag in the start script.

Can this information help?

dia@lenovo:~/NANO-D/SAMSON/0.7.0/Binaries$ ./SAMSON-Core.sh 
saving context
launching SAMSON-Core
Python found in the system: 
Python executable:    /usr/bin/python3
qt.network.ssl: QSslSocket: cannot resolve CRYPTO_num_locks
qt.network.ssl: QSslSocket: cannot resolve CRYPTO_set_id_callback
qt.network.ssl: QSslSocket: cannot resolve CRYPTO_set_locking_callback
qt.network.ssl: QSslSocket: cannot resolve ERR_free_strings
qt.network.ssl: QSslSocket: cannot resolve EVP_CIPHER_CTX_cleanup
qt.network.ssl: QSslSocket: cannot resolve EVP_CIPHER_CTX_init
qt.network.ssl: QSslSocket: cannot resolve sk_new_null
qt.network.ssl: QSslSocket: cannot resolve sk_push
qt.network.ssl: QSslSocket: cannot resolve sk_free
qt.network.ssl: QSslSocket: cannot resolve sk_num
qt.network.ssl: QSslSocket: cannot resolve sk_pop_free
qt.network.ssl: QSslSocket: cannot resolve sk_value
qt.network.ssl: QSslSocket: cannot resolve SSL_library_init
qt.network.ssl: QSslSocket: cannot resolve SSL_load_error_strings
qt.network.ssl: QSslSocket: cannot resolve SSL_get_ex_new_index
qt.network.ssl: QSslSocket: cannot resolve SSLv3_client_method
qt.network.ssl: QSslSocket: cannot resolve SSLv23_client_method
qt.network.ssl: QSslSocket: cannot resolve SSLv3_server_method
qt.network.ssl: QSslSocket: cannot resolve SSLv23_server_method
qt.network.ssl: QSslSocket: cannot resolve X509_STORE_CTX_get_chain
qt.network.ssl: QSslSocket: cannot resolve OPENSSL_add_all_algorithms_noconf
qt.network.ssl: QSslSocket: cannot resolve OPENSSL_add_all_algorithms_conf
qt.network.ssl: QSslSocket: cannot resolve SSLeay
qt.network.ssl: QSslSocket: cannot resolve SSLeay_version
qt.network.ssl: QSslSocket: cannot call unresolved function SSLeay
qt.network.ssl: Incompatible version of OpenSSL
libpng warning: iCCP: known incorrect sRGB profile
=============== SBGPath summary infos ================

===============
 > SBGPath::getSAMSONPath()                       = /home/dia/NANO-D/SAMSON/0.7.0
 > SBGPath::getSDKPath()                          = .
===============
 > SBGPath::getUserDataPath()                     = /home/dia/NANO-D/SAMSON
 > SBGPath::getUserElementPath()                  = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Elements
 > SBGPath::getUserElementDataPath()              = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Data/Elements
 > SBGPath::getUserDownloadedElementPath()        = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Download/Elements
===============
 > SBGPath::getDevelopperDataPath()               = 
 > SBGPath::getDevelopperElementPath()            = /Elements
 > SBGPath::getDevelopperElementPackagedPath()    = /Connect/Elements
===============
 > SBGPath::getBinaryPath()                       = /home/dia/NANO-D/SAMSON/0.7.0/Binaries
===============
 > SBGPath::getCurrentSkinPath()                  = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default
 > SBGPath::getCursorPath()                       = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/Cursors
 > SBGPath::getIconPath()                         = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/Icons
 > SBGPath::getImagePath()                        = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/Images
 > SBGPath::getSoundPath()                        = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/Sounds
 > SBGPath::getSplashScreenPath()                 = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/SplashScreens
 > SBGPath::getStylePath()                        = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/StyleSheets
===============
 > SBGPath::getInterfacePath()                    = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Interface
 > SBGPath::getScratchPath()                      = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch
 > SBGPath::getScratchElementPath()               = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements
 > SBGPath::getScratchUpdatesPath()               = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Updates
 > SBGPath::getShaderPath()                       = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Shaders
 > SBGPath::getTranslationPath()                  = /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Translations

=============== SBGPath summary infos ================

"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/Cursors"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/Icons"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Elements"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Shaders"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/Sounds"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/SplashScreens"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Skins/Default/StyleSheets"
"/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Resource/Translations"

=============================================================================
Allowed elements ids in database: 
1   ->   "06485695-DEE2-1383-A575-E5AABA05DCCD"
2   ->   "154ACCDA-8950-C6B2-7456-DAB6BA82AA5D"
3   ->   "2305E415-C812-1C1A-CDBE-78896176B067"
4   ->   "385FE362-ADFD-CE55-95C0-4E63560EFA29"
5   ->   "8B38B2FD-DE8D-F24A-36E7-7AC624173F9F"
6   ->   "8CBDC8B1-59E1-6459-D68F-B840275DD5E9"
7   ->   "9DFF7162-FFBF-C149-C9D3-2E1DEBC40321"
8   ->   "CE375B52-7D0B-7DF0-AA3E-EB0AD85BEBFE"
9   ->   "CEBACCDA-8950-C6B2-7456-D077BA82AA5D"
10   ->   "EC83FAEB-1A42-FF16-EEB2-CF021EF38EBF"
11   ->   "F912F119-7CBB-B5BD-972A-0A02DFCF683D"
=============================================================================

"start 0 0 files downloaded successfully\n"
Could not open  "/home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/disabledElements.info"
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/06485695-DEE2-1383-A575-E5AABA05DCCD
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/154ACCDA-8950-C6B2-7456-DAB6BA82AA5D
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/2305E415-C812-1C1A-CDBE-78896176B067
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/385FE362-ADFD-CE55-95C0-4E63560EFA29
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/8B38B2FD-DE8D-F24A-36E7-7AC624173F9F
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/8CBDC8B1-59E1-6459-D68F-B840275DD5E9
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/9DFF7162-FFBF-C149-C9D3-2E1DEBC40321
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/CE375B52-7D0B-7DF0-AA3E-EB0AD85BEBFE
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/CEBACCDA-8950-C6B2-7456-D077BA82AA5D
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/EC83FAEB-1A42-FF16-EEB2-CF021EF38EBF
Extracting /home/dia/.NANO-D/SAMSON/DATA/0.7.0/Scratch/Elements/F912F119-7CBB-B5BD-972A-0A02DFCF683D
Registering: A visual model to represent secondary structure
	Registering: Secondary structure
Registering: This element contains three exporters (*xyz, *.pdb, *.mol2) to easily export models from SAMSON
	Registering: Protein Data Bank (*.pdb)
	Registering: XYZ (*.xyz)
	Registering: Mol2 (*.mol2)
Registering: An editor to generate atoms from the periodic table
	Registering: Periodic table
Registering: An editor to easily twist molecular systems
	Registering: Twister
Registering: This element contains a set of essential editors for SAMSON, for example to select, translate, erase, rotate...
	Registering: Translation controller plane
	Registering: Torsion
	Registering: Ruler
	Registering: Delegate
	Registering: Translation controller center GUI
	Registering: Rotation controller axis
	Registering: Translation controller plane GUI
	Registering: Rotation controller axis GUI
	Registering: Angle
	Registering: Atom-atom distance
	Registering: Atom name
	Registering: Translation controller axis
	Registering: Translation controller center
	Registering: Translation
	Registering: Eraser
	Registering: Rotation controller
	Registering: Translation controller axis GUI
	Registering: Bond order
	Registering: Group name
	Registering: Translation controller
	Registering: Move camera
	Registering: Atom creator
	Registering: Rotation controller track-ball GUI
	Registering: Bond length
	Registering: Rotation controller track-ball
	Registering: Rectangle selection
	Registering: Lasso selection
	Registering: Point selection
	Registering: Rotation
Registering: This element is a group called default visual models to easily display different molecule visualizations in SAMSON
	Registering: Gaussian surface
	Registering: Ball and stick
	Registering: Ball-and-stick
	Registering: Van der Waals
	Registering: Lines
	Registering: Licorice
	Registering: Lines
	Registering: Van der Waals
	Registering: Gaussian surface
	Registering: Licorice
Registering: SAMSON document exporters (*.sam and *.samx)
	Registering: SAMSON Documents (*.samx)
	Registering: SAMSON Documents (*.sam)
Registering: This element contains three importers (*xyz, *.mol2, *.pdb [with aliases: *.pdb1, ..., *.pdb6, *.ent, *.vdb]) to easily load models into SAMSON
	Registering: Protein Data Bank (*.pdb4)
	Registering: Protein Data Bank (*.ent)
	Registering: Protein Data Bank (*.pdb5)
	Registering: VIPERdb, PDB format (*.vdb)
	Registering: Protein Data Bank (*.pdb6)
	Registering: XYZ (*.xyz)
	Registering: Protein Data Bank (*.pdb)
	Registering: Mol2 (*.mol2)
	Registering: Protein Data Bank (*.pdb1)
	Registering: Protein Data Bank (*.pdb2)
	Registering: Protein Data Bank (*.pdb3)
Registering: SAMSON document importers (*.sam and *.samx)
	Registering: SAMSON Documents (*.samx)
	Registering: SAMSON Documents (*.sam)
Registering: Universal Force Field
	Registering: Universal Force Field
	Registering: Universal Force Field
	Registering: UFF Force Field Factory
Registering: An element containing six state updaters
	Registering: SESStateUpdaterPack
	Registering: SESStateUpdaterPack
	Registering: Partitioned Euler
	Registering: SESStateUpdaterPack
	Registering: Velocity Verlet
	Registering: SESStateUpdaterPack
	Registering: Adaptively restrained NVE
	Registering: Steepest descent
	Registering: SESStateUpdaterPack
	Registering: SESStateUpdaterPack
	Registering: Interactive modeling
	Registering: Adaptive steepest descent
Registering: SAMSON Base - Data Model - App
	Registering: App
Registering: SAMSON Base - Data Model - Color
	Registering: Color scheme per chain ID
	Registering: Constant color scheme
	Registering: Color scheme per temperature factor
	Registering: CPK color scheme
	Registering: Color scheme per residue sequence number
	Registering: Color scheme per residue type
	Registering: Color scheme per partial charge
	Registering: Color scheme per secondary structure type
	Registering: Color scheme per occupancy
	Registering: Color scheme per formal charge
Registering: SAMSON Base - Data Model - Data Graph
	Registering: Data graph node
	Registering: Node group
	Registering: Data graph node color scheme
Registering: SAMSON Base - Data Model - Document
	Registering: Label
	Registering: Camera
	Registering: Layer
	Registering: Document
Registering: SAMSON Base - Data Model - Structural Model
	Registering: Molecule
	Registering: Backbone
	Registering: Atom
	Registering: Segment
	Registering: Bond
	Registering: Side chain
	Registering: Path
	Registering: Chain
	Registering: Structural model
	Registering: Grid
	Registering: Structural particle
	Registering: Residue
	Registering: Structural nodes
	Registering: Conformation
	Registering: Pseudo-atom
	Registering: Structural group
Registering: SAMSON Base - Data Model - Visual Model
Registering: SAMSON Base - Data Model - Controller
	Registering: Controller
	Registering: Controller node
Registering: SAMSON Base - GUI - DataGraph
Registering: SAMSON Base - GUI - Document
	Registering: The GUI of a camera
	Registering: The GUI of a layer
Registering: SAMSON Base - GUI - Editor
	Registering: Editor
Registering: SAMSON Base - GUI - Inspector
	Registering: Inspector - SBQuantity::mass Factory
	Registering: Inspector - SBQuantity::length Factory
	Registering: Inspector - Bool Factory
	Registering: Inspector - Node Factory
	Registering: Inspector - SBBond::BondType Factory
	Registering: Inspector - SBQuantity::dimensionless Factory
	Registering: Inspector - int Factory
	Registering: Inspector - SBNode::Type Factory
	Registering: Inspector - double Factory
	Registering: Inspector - SBResidue::ResidueType Factory
	Registering: Inspector - std::string Factory
	Registering: Inspector - float Factory
	Registering: Inspector - SBQuantity::second Factory
	Registering: Inspector - unsigned short Factory
	Registering: Inspector - SBPosition3 Factory
	Registering: Inspector - short Factory
	Registering: Inspector - char Factory
	Registering: Inspector - SBVector3 Factory
	Registering: Inspector - SBQuantity::dimensionless Factory
	Registering: Inspector - unsigned int Factory
	Registering: Inspector - Atom Factory
	Registering: Inspector - SBResidue::SecondaryStructureType Factory
	Registering: Inspector - SBPath::AnimationType Factory
	Registering: Inspector - SBElement::Type Factory
	Registering: Inspector - SBQuantity::time Factory
	Registering: Inspector - char Factory
Registering: SAMSON Base - GUI - Structural model
	Registering: The GUI of an atom
	Registering: The GUI of a structural model
	Registering: The GUI of a structural model conformation
	Registering: The GUI of a bond
	Registering: The GUI of a structural model conformation
Registering: SAMSON Base - Facade - SAMSON
	Registering: The SAMSON Facade
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile

=============================================================================
Allowed elements in database: 

      -----------------------------------------------------------------------
      -  "elementName" "Secondary structure on GPUs"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "06485695-DEE2-1383-A575-E5AABA05DCCD"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "SAMSON Visual Models"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "154ACCDA-8950-C6B2-7456-DAB6BA82AA5D"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "Periodic table"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "2305E415-C812-1C1A-CDBE-78896176B067"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "Basic importers"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "385FE362-ADFD-CE55-95C0-4E63560EFA29"
      -  "elementVersion" "0.7.7"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "Twister"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "8B38B2FD-DE8D-F24A-36E7-7AC624173F9F"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "Universal force field"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "8CBDC8B1-59E1-6459-D68F-B840275DD5E9"
      -  "elementVersion" "0.7.5"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "SAMSON Format Exporter"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "9DFF7162-FFBF-C149-C9D3-2E1DEBC40321"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "SAMSON Format importers"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "CE375B52-7D0B-7DF0-AA3E-EB0AD85BEBFE"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "SAMSON Editors"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "CEBACCDA-8950-C6B2-7456-D077BA82AA5D"
      -  "elementVersion" "0.7.3"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "Basic exporters"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "EC83FAEB-1A42-FF16-EEB2-CF021EF38EBF"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------

      -----------------------------------------------------------------------
      -  "elementName" "State Updater Pack"
      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
      -  "elementID" "F912F119-7CBB-B5BD-972A-0A02DFCF683D"
      -  "elementVersion" "0.7.0"
      -  "checksumDebug" 0
      -  "checksumRelease" 0
      -  "elementDescription" ""
      -  "elementOS" ""
      -  "samsonVersion" "0.7.0"
      -  "forceUpdate" false
      -----------------------------------------------------------------------
=============================================================================

QPixmap::scaled: Pixmap is a null pixmap
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
"File"
"File"
"Edit"
"Edit"
"App"

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 10:30:03 GMT

DmitriyMarin — Fri, 01 Mar 2019 10:30:03 GMT

@Ivan
Unfortunately, I do not have a laptop with linux and an Nvidia Optimus GPU now.

Do you have the Nouveau driver blacklisted or uninstalled? Because it causes some issues on Nvidia Optimus GPUs.
Does optimus/bumblebee work for you in other apps? What happens if you, for example, execute in the terminal:

optirun glxgears

Does primusrun work for you? optirun relies on VirtualGL which might cause the issue you have.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Fri, 01 Mar 2019 07:39:43 GMT

Ivan — Fri, 01 Mar 2019 07:39:43 GMT

@dmitriymarin

dia@lenovo:~/NANO-D/SAMSON/0.7.0/Binaries$ ldd ./SAMSON-Core | grep gl
	libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007fa0eba45000)
dia@lenovo:~/NANO-D/SAMSON/0.7.0/Binaries$ ldd ./SAMSON-Core | grep GL
	libOpenGL.so.0 => /usr/lib/x86_64-linux-gnu/libOpenGL.so.0 (0x00007fdd14161000)
	libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007fdd13f2f000)
	libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007fdd13cc0000)
	libSBGLog.so => not found
	libQt5OpenGL.so.5 => /usr/lib/x86_64-linux-gnu/libQt5OpenGL.so.5 (0x00007fdd13c66000)
	libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007fdd121e6000)
	libGL.so.1 => /usr/lib/x86_64-linux-gnu/libGL.so.1 (0x00007fdd117e4000)
dia@lenovo:~/NANO-D/SAMSON/0.7.0/Binaries$ optirun glxinfo | grep OpenGL
OpenGL vendor string: NVIDIA Corporation
OpenGL renderer string: GeForce GTX 1050/PCIe/SSE2
OpenGL core profile version string: 4.5.0 NVIDIA 390.87
OpenGL core profile shading language version string: 4.50 NVIDIA
OpenGL core profile context flags: (none)
OpenGL core profile profile mask: core profile
OpenGL core profile extensions:
OpenGL version string: 4.6.0 NVIDIA 390.87
OpenGL shading language version string: 4.60 NVIDIA
OpenGL context flags: (none)
OpenGL profile mask: (none)
OpenGL extensions:

dia@lenovo:~/NANO-D/SAMSON/0.7.0/Binaries$ optirun ldd ./SAMSON-Core | grep gl
	libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f21ab7ff000)
dia@lenovo:~/NANO-D/SAMSON/0.7.0/Binaries$ optirun ldd ./SAMSON-Core | grep GL
	libOpenGL.so.0 => /usr/lib/x86_64-linux-gnu/libOpenGL.so.0 (0x00007f440f894000)
	libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007f440f662000)
	libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007f440f3f3000)
	libSBGLog.so => not found
	libQt5OpenGL.so.5 => /usr/lib/x86_64-linux-gnu/libQt5OpenGL.so.5 (0x00007f440f399000)
	libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007f440d915000)
	libGL.so.1 => /usr/lib/x86_64-linux-gnu/primus/libGL.so.1 (0x00007f440cf62000)

about libGL version. I can provide synaptic screenshot.

Reply to SAMSON with hybrid graphics cards (Intel/Nvidia) on Thu, 28 Feb 2019 17:59:01 GMT

DmitriyMarin — Thu, 28 Feb 2019 17:59:01 GMT

Thank you @Ivan for reporting this issue!

It might be a problem specific to optirun or to OpenGL. Do you have libGL installed via nvidia drivers or mesa-utils?

Could you, please, check dependencies for SAMSON-Core:

cd ~/NANO-D/SAMSON/0.7.0/Binaries
ldd ./SAMSON-Core | grep gl
ldd ./SAMSON-Core | grep GL

In particular, is libGL.so.1 the correct one?

And could you, please, run and post the output for

optirun glxinfo | grep OpenGL