External Email - Use Caution
Hello Torkil, Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from https://secure-web.cisco.com/11eosYMqxQIzJXYwfskbMMIPybJKGeVS7FnOZrEup8mvl0_.... There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build. - R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard <torkil@drcmr.dk> wrote: External Email - Use Caution Hi RuopengThe users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.Mvh.TorkilOn 26/04/2021 19.16, Wang, Ruopeng wrote:Hi Torkil,Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?Best,RuopengOn Apr 26, 2021, at 6:06 AM, Torkil Svensgaard <torkil@drcmr.dk> wrote: External Email - Use CautionHiWe have an older Ubuntu 16.04 HPC installation on which Freeview runsjust fine. We also have a brand new CentOS 8 Stream HPC installationwith much better hardware on which Freeview slows to a crawl after a bitof use.There's no error as such, it just slows to the point of being unusable.Any suggestions on how to fix it, or pinpoint the cause?Thanks,Torkil_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1iIikemoA9DiusPW-kySeM7Lhv0S5lGLLVKXGGnBXsLSRp74...;. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote:
External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK... https://secure-web.cisco.com/11eosYMqxQIzJXYwfskbMMIPybJKGeVS7FnOZrEup8mvl0_xfAq3vjTQd-e0eiOGTDacIj_SAHaTlklHvVT7UJLV4Ng-yu0B4D36lSgtCjOwEoU0USFCfuKCU44sfK_UDlvhO05uNjj3gGp4qmWavfc90C6CqdF24OsTPBw6lj1lo3dMvWmY-D9xl3oAD0gx8_XmNegRGP6qgyi_3FD9DiFvjNTCPhzQQqUCoz6LQPup60qbCkKXMoXG6KMA-OhLf3Ysvmo7TrN9eWe_dxTDMUw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F. There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote:
Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wOjN8ftqgihzT7a9Xbkzhxtt6__qadLT0dmRgDscQKZD8v... https://secure-web.cisco.com/18-3eBByYHzbV-9MLBagdO4nSPj4NRA2HMKD1FHgrroBir6DFimC_QCy9WNrfug63h9QRN9nut5bnxN35AWGU-2zLloooMzTPt-FLZHhLL_7a29OXtTcqLofkJd_A8ZGKNhg6ZYb6pQkz6-Uz05DIYp73emFDWdR8LzPMAPebuEDb4Z7W1lXeCrI6GmMRdxOuWx1EoH00o-G8T3PQV_1R69oIXF8sTDNW88sHpOLsyXQYcXVYLhlfX_aqRsBkPsqO9X23RD78yb71dXvBZ75b3w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1wOjN8ftqgihzT7a9Xbkzhxtt6__qadLT0dmRgDscQKZD8v...
External Email - Use Caution
Hi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote:
External Email - Use CautionHi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote:
External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK... https://secure-web.cisco.com/11eosYMqxQIzJXYwfskbMMIPybJKGeVS7FnOZrEup8mvl0_xfAq3vjTQd-e0eiOGTDacIj_SAHaTlklHvVT7UJLV4Ng-yu0B4D36lSgtCjOwEoU0USFCfuKCU44sfK_UDlvhO05uNjj3gGp4qmWavfc90C6CqdF24OsTPBw6lj1lo3dMvWmY-D9xl3oAD0gx8_XmNegRGP6qgyi_3FD9DiFvjNTCPhzQQqUCoz6LQPup60qbCkKXMoXG6KMA-OhLf3Ysvmo7TrN9eWe_dxTDMUw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F. There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote:
Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr..mgh.harvard.edu https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1q5cwqIS5zhgiPTcSkVXCLf0Prye5fkTAPYQ25gz_UGLCNsy... http://secure-web.cisco.com/1iIikemoA9DiusPW-kySeM7Lhv0S5lGLLVKXGGnBXsLSRp74JoEwyZECaDJe2aKVIQOIs8cOgEpF8stXM_2tGIO0KcGv9VGtX-Pck6nEEDPqOabMy1IbD-UvlmWFVd3at2SCZcMbc6Va5Qk48zzQZqonftcwqFl8aOd9YNWjgxtb_diWkUexjHZFfvXgjEggnb9MqNb_4rVItny0qIfpzXbiDtk2KJuXHMA1lyUZRd0ggdcg9C9fIv8BTMva6qTMyV16aNQkPAdZgNGL712FctA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wOjN8ftqgihzT7a9Xbkzhxtt6__qadLT0dmRgDscQKZD8v... https://secure-web.cisco.com/18-3eBByYHzbV-9MLBagdO4nSPj4NRA2HMKD1FHgrroBir6DFimC_QCy9WNrfug63h9QRN9nut5bnxN35AWGU-2zLloooMzTPt-FLZHhLL_7a29OXtTcqLofkJd_A8ZGKNhg6ZYb6pQkz6-Uz05DIYp73emFDWdR8LzPMAPebuEDb4Z7W1lXeCrI6GmMRdxOuWx1EoH00o-G8T3PQV_1R69oIXF8sTDNW88sHpOLsyXQYcXVYLhlfX_aqRsBkPsqO9X23RD78yb71dXvBZ75b3w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1NmMfSt3ppP0X9CKAdvh6VN5XUOAuFW4hvFGoJnH-LVdl8y...
So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use CautionHi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote:
External Email - Use CautionHi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote:
External Email - Use CautionHello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK... https://secure-web.cisco.com/11eosYMqxQIzJXYwfskbMMIPybJKGeVS7FnOZrEup8mvl0_xfAq3vjTQd-e0eiOGTDacIj_SAHaTlklHvVT7UJLV4Ng-yu0B4D36lSgtCjOwEoU0USFCfuKCU44sfK_UDlvhO05uNjj3gGp4qmWavfc90C6CqdF24OsTPBw6lj1lo3dMvWmY-D9xl3oAD0gx8_XmNegRGP6qgyi_3FD9DiFvjNTCPhzQQqUCoz6LQPup60qbCkKXMoXG6KMA-OhLf3Ysvmo7TrN9eWe_dxTDMUw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F. There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use CautionHi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote:
Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use CautionHi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Hi
It the same on every login server. Running locally inside at Thinlinc session.
Mvh.
Torkil
On 29/04/2021 15.05, Wang, Ruopeng wrote:
So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use CautionHi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote:
External Email - Use CautionHi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote:
External Email - Use CautionHello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK... https://secure-web.cisco.com/11eosYMqxQIzJXYwfskbMMIPybJKGeVS7FnOZrEup8mvl0_xfAq3vjTQd-e0eiOGTDacIj_SAHaTlklHvVT7UJLV4Ng-yu0B4D36lSgtCjOwEoU0USFCfuKCU44sfK_UDlvhO05uNjj3gGp4qmWavfc90C6CqdF24OsTPBw6lj1lo3dMvWmY-D9xl3oAD0gx8_XmNegRGP6qgyi_3FD9DiFvjNTCPhzQQqUCoz6LQPup60qbCkKXMoXG6KMA-OhLf3Ysvmo7TrN9eWe_dxTDMUw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F. There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use CautionHi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote:
Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
> On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote: > > External Email - Use Caution > > Hi > > We have an older Ubuntu 16.04 HPC installation on which Freeview runs > just fine. We also have a brand new CentOS 8 Stream HPC installation > with much better hardware on which Freeview slows to a crawl after a bit > of use. > > There's no error as such, it just slows to the point of being unusable. > > Any suggestions on how to fix it, or pinpoint the cause? > > Thanks, > > Torkil > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... > https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Hi again
Also the same when run via X11 from a beastly compute node.
As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess.
Anyone using it on CentOS 8 Stream with success?
Mvh.
Torkil
On 29/04/2021 23.09, Torkil Svensgaard wrote:
Hi
It the same on every login server. Running locally inside at Thinlinc session.
Mvh.
Torkil
On 29/04/2021 15.05, Wang, Ruopeng wrote:
So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote:
External Email - Use Caution
Hi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote:
External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK...
There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote: > Hi Torkil, > > Can you tell what part of the program slows down the most? Data > loading? GUI responsiveness? Image/3D rendering? Or just in general? > If it is the rendering, maybe try updating the graphics card driver > to the latest? > > Best, > Ruopeng > >> On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk >> wrote: >> >> External Email - Use Caution >> >> Hi >> >> We have an older Ubuntu 16.04 HPC installation on which Freeview >> runs >> just fine. We also have a brand new CentOS 8 Stream HPC >> installation >> with much better hardware on which Freeview slows to a crawl >> after a bit >> of use. >> >> There's no error as such, it just slows to the point of being >> unusable. >> >> Any suggestions on how to fix it, or pinpoint the cause? >> >> Thanks, >> >> Torkil >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... >> >> https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr..mgh.harvard.edu > https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH... > > https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > The information in this e-mail is intended only for the person to > whom it is addressed. If you believe this e-mail was sent to you in > error and the e-mail contains patient information, please contact > the > Mass General Brigham Compliance HelpLine at*MailScanner has detected > a possible fraud attempt from "secure-web.cisco.com" claiming to be* > http://secure-web.cisco.com/1q5cwqIS5zhgiPTcSkVXCLf0Prye5fkTAPYQ25gz_UGLCNsy... > > http://secure-web.cisco.com/1iIikemoA9DiusPW-kySeM7Lhv0S5lGLLVKXGGnBXsLSRp74JoEwyZECaDJe2aKVIQOIs8cOgEpF8stXM_2tGIO0KcGv9VGtX-Pck6nEEDPqOabMy1IbD-UvlmWFVd3at2SCZcMbc6Va5Qk48zzQZqonftcwqFl8aOd9YNWjgxtb_diWkUexjHZFfvXgjEggnb9MqNb_4rVItny0qIfpzXbiDtk2KJuXHMA1lyUZRd0ggdcg9C9fIv8BTMva6qTMyV16aNQkPAdZgNGL712FctA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline. > > If the e-mail was sent to you in error but does not contain patient > information, please contact the sender and properly dispose of the > e-mail. > Please note that this e-mail is not secure (encrypted). If you do > not wish to continue communication over unencrypted e-mail, please > notify the sender of this message immediately. Continuing to > send or > respond to e-mail after receiving this message means you understand > and accept this risk and wish to continue to communicate over > unencrypted e-mail. >
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HI Torkil,
We tested on our CentOS 8 machines as well as CentOS 8 VM but did not notice any slow-down. I personally run freeview remotely on a CentOS 8 machine occasionally and have never experience such an issue. I’m at a loss, too. :( I’m just shooting in the dark now - as I mentioned before, have you tried updating your graphics card driver? I remember quite a while ago we once had a slow-down issue on one of our machines. It turned out to be a conflict between the graphics card driver and the vtk engine we used (not sure whose fault it was). After updating the driver the problem went away.
Ruopeng
On May 4, 2021, at 2:44 AM, Torkil Svensgaard <torkil@drcmr.dkmailto:torkil@drcmr.dk> wrote:
External Email - Use Caution
Hi again
Also the same when run via X11 from a beastly compute node.
As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess.
Anyone using it on CentOS 8 Stream with success?
Mvh.
Torkil
On 29/04/2021 23.09, Torkil Svensgaard wrote: Hi
It the same on every login server. Running locally inside at Thinlinc session.
Mvh.
Torkil
On 29/04/2021 15.05, Wang, Ruopeng wrote: So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard <torkil@drcmr.dkmailto:torkil@drcmr.dk> wrote:
External Email - Use Caution
Hi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote: External Email - Use Caution
Hi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote: External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.comhttp://secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK...
There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote: Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH...
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1q5cwqIS5zhgiPTcSkVXCLf0Prye5fkTAPYQ25gz_UGLCNsy...
If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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External Email - Use Caution
Hi Ruopeng
All the boxes are fully upgraded. Some of them have an Nvidia GPU and some of them only have onboard video, but the problem is the same on all of them, so probably not that.
I sent you a callgrind file from one of my users, I hope that can provide some insigts.
Thanks,
Torkil
On 2021-05-04 15:11, Wang, Ruopeng wrote:
HI Torkil,
We tested on our CentOS 8 machines as well as CentOS 8 VM but did not notice any slow-down. I personally run freeview remotely on a CentOS 8 machine occasionally and have never experience such an issue. I’m at a loss, too. :( I’m just shooting in the dark now - as I mentioned before, have you tried updating your graphics card driver? I remember quite a while ago we once had a slow-down issue on one of our machines. It turned out to be a conflict between the graphics card driver and the vtk engine we used (not sure whose fault it was). After updating the driver the problem went away.
Ruopeng
On May 4, 2021, at 2:44 AM, Torkil Svensgaard torkil@drcmr.dk wrote: External Email - Use Caution
Hi again
Also the same when run via X11 from a beastly compute node.
As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess.
Anyone using it on CentOS 8 Stream with success?
Mvh.
Torkil
On 29/04/2021 23.09, Torkil Svensgaard wrote: Hi
It the same on every login server. Running locally inside at Thinlinc session.
Mvh.
Torkil
On 29/04/2021 15.05, Wang, Ruopeng wrote: So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote: External Email - Use Caution
Hi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote: External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com [1]" claiming to be*
https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK...
There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote: Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr..mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be*
http://secure-web.cisco.com/1q5cwqIS5zhgiPTcSkVXCLf0Prye5fkTAPYQ25gz_UGLCNsy...
If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/14KYmpxA4g2HT30QVDErT5H-c2VyJQaxWmK6pRWUACXJm7g5... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not
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Links:
[1] http://secure-web.cisco.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ao3sKQK7fs7qxqnD2qA3fxZ3cdcK03Zh-FjobUlsEDzzzh... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1BYruLI95mUO9Wsaev5YPaURt6vUhAmXFHiNXENg0B5PQj-l... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Thanks for the file. Did the user experience slow-down while generating the profile (other than the slow-down by valgrind)?
Ruopeng
On May 5, 2021, at 7:40 AM, Torkil Svensgaard <torkil@drcmr.dkmailto:torkil@drcmr.dk> wrote:
External Email - Use Caution
Hi Ruopeng
All the boxes are fully upgraded. Some of them have an Nvidia GPU and some of them only have onboard video, but the problem is the same on all of them, so probably not that.
I sent you a callgrind file from one of my users, I hope that can provide some insigts.
Thanks,
Torkil
On 2021-05-04 15:11, Wang, Ruopeng wrote: HI Torkil,
We tested on our CentOS 8 machines as well as CentOS 8 VM but did not notice any slow-down. I personally run freeview remotely on a CentOS 8 machine occasionally and have never experience such an issue. I’m at a loss, too. :( I’m just shooting in the dark now - as I mentioned before, have you tried updating your graphics card driver? I remember quite a while ago we once had a slow-down issue on one of our machines. It turned out to be a conflict between the graphics card driver and the vtk engine we used (not sure whose fault it was). After updating the driver the problem went away.
Ruopeng
On May 4, 2021, at 2:44 AM, Torkil Svensgaard <torkil@drcmr.dkmailto:torkil@drcmr.dk> wrote: External Email - Use Caution
Hi again
Also the same when run via X11 from a beastly compute node.
As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess.
Anyone using it on CentOS 8 Stream with success?
Mvh.
Torkil
On 29/04/2021 23.09, Torkil Svensgaard wrote: Hi
It the same on every login server. Running locally inside at Thinlinc session.
Mvh.
Torkil
On 29/04/2021 15.05, Wang, Ruopeng wrote: So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard <torkil@drcmr.dkmailto:torkil@drcmr.dk> wrote:
External Email - Use Caution
Hi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote: External Email - Use Caution
Hi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote: External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.comhttp://secure-web.cisco.com/ [1]" claiming to be*
https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK...
There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote: Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr..mgh.harvard.edu
https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be*
http://secure-web.cisco.com/1q5cwqIS5zhgiPTcSkVXCLf0Prye5fkTAPYQ25gz_UGLCNsy...
If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wOjN8ftqgihzT7a9Xbkzhxtt6__qadLT0dmRgDscQKZD8v...
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1OzThYVp1mjH5esfWVFDavz5wDLWDn-6xYAw8kbe72wJSx0... The information in this e-mail is intended only for the person to whom
it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/14KYmpxA4g2HT30QVDErT5H-c2VyJQaxWmK6pRWUACXJm7g5... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not
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Links: ------ [1] http://secure-web.cisco.comhttp://secure-web.cisco.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ao3sKQK7fs7qxqnD2qA3fxZ3cdcK03Zh-FjobUlsEDzzzh... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1BYruLI95mUO9Wsaev5YPaURt6vUhAmXFHiNXENg0B5PQj-l... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Hi Ruopeng
He did.
" On 2021-05-05 13:31, Torkil Svensgaard wrote:
Perfect, thanks. Did it go stall slow while capturing, or just a bit slow from valgrind overhead?
I would say it was 90% of the worst I've seen. Didn't want to push more, was afraid it's going to force quit again. "
Mvh.
Torkil
On 05/05/2021 16.32, Wang, Ruopeng wrote:
Thanks for the file. Did the user experience slow-down while generating the profile (other than the slow-down by valgrind)?
Ruopeng
On May 5, 2021, at 7:40 AM, Torkil Svensgaard <torkil@drcmr.dk mailto:torkil@drcmr.dk> wrote:
External Email - Use Caution
Hi Ruopeng
All the boxes are fully upgraded. Some of them have an Nvidia GPU and some of them only have onboard video, but the problem is the same on all of them, so probably not that.
I sent you a callgrind file from one of my users, I hope that can provide some insigts.
Thanks,
Torkil
On 2021-05-04 15:11, Wang, Ruopeng wrote:
HI Torkil,
We tested on our CentOS 8 machines as well as CentOS 8 VM but did not notice any slow-down. I personally run freeview remotely on a CentOS 8 machine occasionally and have never experience such an issue. I’m at a loss, too. :( I’m just shooting in the dark now - as I mentioned before, have you tried updating your graphics card driver? I remember quite a while ago we once had a slow-down issue on one of our machines. It turned out to be a conflict between the graphics card driver and the vtk engine we used (not sure whose fault it was). After updating the driver the problem went away.
Ruopeng
On May 4, 2021, at 2:44 AM, Torkil Svensgaard <torkil@drcmr.dk mailto:torkil@drcmr.dk> wrote: External Email - Use Caution
Hi again
Also the same when run via X11 from a beastly compute node.
As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess.
Anyone using it on CentOS 8 Stream with success?
Mvh.
Torkil
On 29/04/2021 23.09, Torkil Svensgaard wrote: Hi
It the same on every login server. Running locally inside at Thinlinc session.
Mvh.
Torkil
On 29/04/2021 15.05, Wang, Ruopeng wrote: So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard <torkil@drcmr.dk mailto:torkil@drcmr.dk> wrote:
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Hi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote: External Email - Use Caution
Hi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote: External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com http://secure-web.cisco.com/[1]" claiming to be*
https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK... https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUKGA68wpQ8QSGMyRuo5dqi6WKrzNk6CWEv3D3k5zgXwVSeUnKbeRMfUPHhP2dywnvdWawfc6hGOU366WlwqrUw9FCRjGeAGc_UxVQOnlVLyo87p5nMa74RlG4twGiXMh54wvDjvt3bRL7G8veAW6UWxddG2PU7QmbmDWGcL0QqQI3v5R4stApLAKQ6b48qDeL3LJC3ZwIR9FbXqj-73ujzq3nj8oO_e1uGuON87bFQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
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Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote: Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
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Hi Torkil,
I just sent you a freeview build for profiling via secure file transferl. Can you run it through valgrind? First please copy it to your freesurfer bin folder $FREESURFER_HOME/bin. Then run this command:
valgrind --tool=callgrind --dump-instr=yes $FREESURFER_HOME/bin/freeview_prof
Load a couple of volumes and/or surfaces, play with it a little bit and close it. There should be a file called callgrind.out.xxxx generated by valgrind. Can you send us the file?
Thanks, Ruopeng
On May 4, 2021, at 2:44 AM, Torkil Svensgaard <torkil@drcmr.dkmailto:torkil@drcmr.dk> wrote:
External Email - Use Caution
Hi again
Also the same when run via X11 from a beastly compute node.
As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess.
Anyone using it on CentOS 8 Stream with success?
Mvh.
Torkil
On 29/04/2021 23.09, Torkil Svensgaard wrote: Hi
It the same on every login server. Running locally inside at Thinlinc session.
Mvh.
Torkil
On 29/04/2021 15.05, Wang, Ruopeng wrote: So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display?
Ruopeng
On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard <torkil@drcmr.dkmailto:torkil@drcmr.dk> wrote:
External Email - Use Caution
Hi again
The user reports freeview being unusable right off the bat this morning.
He left it running in that state, is there anything I can do to capture something that might provide insights?
Mvh.
Torkil
On 28/04/2021 21.24, Torkil Svensgaard wrote: External Email - Use Caution
Hi
We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom.
I installed a dev build this morning and one heavy user reports the following from working with it:
" I used freeview heavily during the day and it worked fine.
Now logged on again (with the same viewer open) and it was impossible to work with.
Even killing it takes forever, and after the window disappears the terminal is still working on something.
Had to also kill the terminal. "
We run Thinlinc as thin client point of entry, freeview is run directly on the login nodes which are fairly beefy things with 256GB RAM.
Mvh.
Torkil
On 27/04/2021 23.12, fsbuild wrote: External Email - Use Caution
Hello Torkil,
Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from *MailScanner has detected a possible fraud attempt from "secure-web.cisco.comhttp://secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fCfSGPn1qXkEuvvvBRvaI4Ptbc4Y_VDhBATIsjsDTPCsUK...
There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build.
- R.
On Apr 27, 2021, at 04:18, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi Ruopeng
The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.
Mvh.
Torkil
On 26/04/2021 19.16, Wang, Ruopeng wrote: Hi Torkil,
Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?
Best, Ruopeng
On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard torkil@drcmr.dk wrote:
External Email - Use Caution
Hi
We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use.
There's no error as such, it just slows to the point of being unusable.
Any suggestions on how to fix it, or pinpoint the cause?
Thanks,
Torkil
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXH...
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1q5cwqIS5zhgiPTcSkVXCLf0Prye5fkTAPYQ25gz_UGLCNsy...
If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wOjN8ftqgihzT7a9Xbkzhxtt6__qadLT0dmRgDscQKZD8v...
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Wang, Ruopeng