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rivetTDA / rivet

RIVET is a tool for Topological Data Analysis, in particular two-parameter persistent homology.
GNU General Public License v3.0
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How long does it take for the example in this page https://rivet.readthedocs.io/en/latest/gettingstarted.html to run? #176

Closed HeJiaxing-hjx closed 1 year ago

HeJiaxing-hjx commented 1 year ago

I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what?

mlesnick commented 1 year ago

It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like?

On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.***> wrote:

I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what?

— Reply to this email directly, view it on GitHub https://github.com/rivetTDA/rivet/issues/176, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

HeJiaxing-hjx commented 1 year ago

It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like? … On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.> wrote: I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what? — Reply to this email directly, view it on GitHub <#176>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.>

Sorry to bother you, but I didn't understand how to open rivet_console, it can't be opened by double clicking. I also tried to enter the terminal and enter the rivet_console command, but it showed command not found.

mlesnick commented 1 year ago

For information about how to use rivet_console, please see the RIVET documentation. If you are not very experienced with Linux command line stuff, it may be helpful to first learn a little about this, e.g., from an online tutorial.

On Thu, Aug 17, 2023 at 3:41 AM hejx1996 @.***> wrote:

It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like? … <#m768513807698997328> On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.> wrote: I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what? — Reply to this email directly, view it on GitHub <#176 https://github.com/rivetTDA/rivet/issues/176>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.>

Sorry to bother you, but I didn't understand how to open rivet_console, it can't be opened by double clicking. I also tried to enter the terminal and enter the rivet_console command, but it showed command not found.

— Reply to this email directly, view it on GitHub https://github.com/rivetTDA/rivet/issues/176#issuecomment-1681795613, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.***>

HeJiaxing-hjx commented 1 year ago

For information about how to use rivet_console, please see the RIVET documentation. If you are not very experienced with Linux command line stuff, it may be helpful to first learn a little about this, e.g., from an online tutorial. … On Thu, Aug 17, 2023 at 3:41 AM hejx1996 @.> wrote: It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like? … <#m768513807698997328> On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.> wrote: I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what? — Reply to this email directly, view it on GitHub <#176 <#176>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.> Sorry to bother you, but I didn't understand how to open rivet_console, it can't be opened by double clicking. I also tried to enter the terminal and enter the rivet_console command, but it showed command not found. — Reply to this email directly, view it on GitHub <#176 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.> Thanks, I'm really not familiar with Ubuntu commands, I'll go and learn. I increase the number in the bin option, and I can run RIVET_GUI although I don't know why.

mlesnick commented 1 year ago

Perhaps it would be helpful for you to tell us (e.g., via screenshots) of exactly what parameters you are using to run rivet_GUI, both when you encounter trouble and when you don't (after increasing the bins). In the former case, are you using the exact same parameters as in the screenshot on the Getting Started page of the RIVET documentation?

On Sun, Aug 20, 2023 at 9:55 PM hejx1996 @.***> wrote:

For information about how to use rivetconsole, please see the RIVET documentation. If you are not very experienced with Linux command line stuff, it may be helpful to first learn a little about this, e.g., from an online tutorial. … <#m-5997085211541396825_> On Thu, Aug 17, 2023 at 3:41 AM hejx1996 @.*> wrote: It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like? … <#m768513807698997328> On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.> wrote: I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what? — Reply to this email directly, view it on GitHub <#176 https://github.com/rivetTDA/rivet/issues/176 <#176 https://github.com/rivetTDA/rivet/issues/176>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.> Sorry to bother you, but I didn't understand how to open rivet_console, it can't be opened by double clicking. I also tried to enter the terminal and enter the rivet_console command, but it showed command not found. — Reply to this email directly, view it on GitHub <#176 (comment) https://github.com/rivetTDA/rivet/issues/176#issuecomment-1681795613>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.***> Thanks, I'm really not familiar with Ubuntu commands, I'll go and learn. I increase the number in the bin option, and I can run RIVET_GUI although I don't know why.

— Reply to this email directly, view it on GitHub https://github.com/rivetTDA/rivet/issues/176#issuecomment-1685502913, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBFA3V53BGYOSJJCVP3XWK52JANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.***>

HeJiaxing-hjx commented 1 year ago

Perhaps it would be helpful for you to tell us (e.g., via screenshots) of exactly what parameters you are using to run rivet_GUI, both when you encounter trouble and when you don't (after increasing the bins). In the former case, are you using the exact same parameters as in the screenshot on the Getting Started page of the RIVET documentation? … On Sun, Aug 20, 2023 at 9:55 PM hejx1996 @.> wrote: For information about how to use rivetconsole, please see the RIVET documentation. If you are not very experienced with Linux command line stuff, it may be helpful to first learn a little about this, e.g., from an online tutorial. … <#m-5997085211541396825_> On Thu, Aug 17, 2023 at 3:41 AM hejx1996 @.> wrote: It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like? … <#m768513807698997328> On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.> wrote: I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what? — Reply to this email directly, view it on GitHub <#176 <#176> <#176 <#176>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.> Sorry to bother you, but I didn't understand how to open rivet_console, it can't be opened by double clicking. I also tried to enter the terminal and enter the rivet_console command, but it showed command not found. — Reply to this email directly, view it on GitHub <#176 (comment) <#176 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.**> Thanks, I'm really not familiar with Ubuntu commands, I'll go and learn. I increase the number in the bin option, and I can run RIVET_GUI although I don't know why. — Reply to this email directly, view it on GitHub <#176 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBFA3V53BGYOSJJCVP3XWK52JANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.>

I followed the instructions to run exactly the same. Later, I changed the memory to 22G, and it worked, then I changed it to 11G, and it worked again. Also, I can run rivet_console with the command sudo ./rivet_console. Thank you for your patience.

mlesnick commented 1 year ago

I am having trouble understanding the problem (it sounds like the example now runs as expected), but my guess is the trouble lies with your virtual machine setup and not with RIVET. I suggest you install RIVET as indicated in the documentation, without the virtual machine.

On Mon, Aug 21, 2023 at 4:27 AM hejx1996 @.***> wrote:

Perhaps it would be helpful for you to tell us (e.g., via screenshots) of exactly what parameters you are using to run rivetGUI, both when you encounter trouble and when you don't (after increasing the bins). In the former case, are you using the exact same parameters as in the screenshot on the Getting Started page of the RIVET documentation? … <#m-1033510168864451484_> On Sun, Aug 20, 2023 at 9:55 PM hejx1996 @.> wrote: For information about how to use rivetconsole, please see the RIVET documentation. If you are not very experienced with Linux command line stuff, it may be helpful to first learn a little about this, e.g., from an online tutorial. … <#m-5997085211541396825_> On Thu, Aug 17, 2023 at 3:41 AM hejx1996 @.> wrote: It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like? … <#m768513807698997328> On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.> wrote: I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what? — Reply to this email directly, view it on GitHub <#176 https://github.com/rivetTDA/rivet/issues/176 <#176 https://github.com/rivetTDA/rivet/issues/176> <#176 https://github.com/rivetTDA/rivet/issues/176 <#176 https://github.com/rivetTDA/rivet/issues/176>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.> Sorry to bother you, but I didn't understand how to open rivet_console, it can't be opened by double clicking. I also tried to enter the terminal and enter the rivet_console command, but it showed command not found. — Reply to this email directly, view it on GitHub <#176 https://github.com/rivetTDA/rivet/issues/176 (comment) <#176 (comment) https://github.com/rivetTDA/rivet/issues/176#issuecomment-1681795613>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.> Thanks, I'm really not familiar with Ubuntu commands, I'll go and learn. I increase the number in the bin option, and I can run RIVET_GUI although I don't know why. — Reply to this email directly, view it on GitHub <#176 (comment) https://github.com/rivetTDA/rivet/issues/176#issuecomment-1685502913>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBFA3V53BGYOSJJCVP3XWK52JANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBFA3V53BGYOSJJCVP3XWK52JANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.>

I followed the instructions to run exactly the same. Later, I changed the memory to 22G, and it worked, then I changed it to 11G, and it worked again. Also, I can run rivet_console with the command sudo ./rivet_console. Thank you for your patience.

— Reply to this email directly, view it on GitHub https://github.com/rivetTDA/rivet/issues/176#issuecomment-1685883078, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBHVPEVMM5SPQWB4CVTXWMLXJANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.***>

HeJiaxing-hjx commented 1 year ago

I am having trouble understanding the problem (it sounds like the example now runs as expected), but my guess is the trouble lies with your virtual machine setup and not with RIVET. I suggest you install RIVET as indicated in the documentation, without the virtual machine. … On Mon, Aug 21, 2023 at 4:27 AM hejx1996 @.> wrote: Perhaps it would be helpful for you to tell us (e.g., via screenshots) of exactly what parameters you are using to run rivetGUI, both when you encounter trouble and when you don't (after increasing the bins). In the former case, are you using the exact same parameters as in the screenshot on the Getting Started page of the RIVET documentation? … <#m-1033510168864451484_> On Sun, Aug 20, 2023 at 9:55 PM hejx1996 @.> wrote: For information about how to use rivetconsole, please see the RIVET documentation. If you are not very experienced with Linux command line stuff, it may be helpful to first learn a little about this, e.g., from an online tutorial. … <#m-5997085211541396825_> On Thu, Aug 17, 2023 at 3:41 AM hejx1996 @.> wrote: It seems unlikely that this would be a memory issue. To pinpoint the problem, it might be helpful to run the same example from the command line, with the same parameters. The documentation explains how to do this. What does the console output look like? … <#m768513807698997328> On Thu, Aug 10, 2023 at 12:14 AM hejx1996 @.> wrote: I successfully installed rivet_GUI on an Ubuntu virtual machine with 11G of memory, but the operation keeps showing zero percent, is it because there is not enough memory or what? — Reply to this email directly, view it on GitHub <#176 <#176> <#176 <#176>> <#176 <#176> <#176 <#176>>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBC3KOBXGIYGKEUGOKDXURNZ5ANCNFSM6AAAAAA3K4R4EE . You are receiving this because you are subscribed to this thread.Message ID: @.> Sorry to bother you, but I didn't understand how to open rivet_console, it can't be opened by double clicking. I also tried to enter the terminal and enter the rivet_console command, but it showed command not found. — Reply to this email directly, view it on GitHub <#176 <#176> (comment) <#176 (comment) <#176 (comment)>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBAPTPV6SO25VD66IX3XVXDJDANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.> Thanks, I'm really not familiar with Ubuntu commands, I'll go and learn. I increase the number in the bin option, and I can run RIVET_GUI although I don't know why. — Reply to this email directly, view it on GitHub <#176 (comment) <#176 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBFA3V53BGYOSJJCVP3XWK52JANCNFSM6AAAAAA3K4R4EE https://github.com/notifications/unsubscribe-auth/AC72KBFA3V53BGYOSJJCVP3XWK52JANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.> I followed the instructions to run exactly the same. Later, I changed the memory to 22G, and it worked, then I changed it to 11G, and it worked again. Also, I can run rivet_console with the command sudo ./rivet_console. Thank you for your patience. — Reply to this email directly, view it on GitHub <#176 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC72KBHVPEVMM5SPQWB4CVTXWMLXJANCNFSM6AAAAAA3K4R4EE . You are receiving this because you commented.Message ID: @.>

Thanks a lot and I will try to install RIVET without the virtual machine.