Details

    • Story Points:
      3
    • Sprint:
      Spring 7 2022 Mar 28 - Apr 8, Spring 8 2022 Apr 11 - Apr 22

      Description

      Please attached report.

      User sent this email:

      My MacBook Pro is macOS Monterey 12.3.1. It is a M1 pro with a Memory of 16GB.

      I installed the most current version of IGB 9.1.10. When I open the RNA seq data, in a few minutes the IGB crashes, shown in a attached file.

      It happens again and again. Now, even I open the IGB without reading and loading any data, it also crashes in several minutes.

      I also installed the SAME IGB in other MacPro macOS Big Sur 11.6, with a processor 2.7 GHz dual core intern core I5 and a memory of 8GB 1867MHz DDR3. The IGB version display 9.1.8. Why it displays different version even I install the same IGB file? However, the IGB does not crash in this computer.

      For this task, determine why the above behavior happened.

      Report from user is attached (see PDF).

        Attachments

          Issue Links

            Activity

            Hide
            nfreese Nowlan Freese added a comment -

            I have contacted the user and asked them to see if IGB 9.1.8 release causes the same crashing on their M1 Mac.

            As the crashing may be due to the new M1 processor on Mac we have decided that it would be a good idea to purchase an M1 Mac for testing purposes. I have emailed Shelley asking to purchase this laptop: https://the-university-of-north-carolina-at-charlotte.shoplightspeed.com/late-2020-13-inch-macbook-air-apple-m1-chip-with-8.html

            This ticket will be updated if the user responds or if we are able to test IGB on the new M1 Mac.

            Show
            nfreese Nowlan Freese added a comment - I have contacted the user and asked them to see if IGB 9.1.8 release causes the same crashing on their M1 Mac. As the crashing may be due to the new M1 processor on Mac we have decided that it would be a good idea to purchase an M1 Mac for testing purposes. I have emailed Shelley asking to purchase this laptop: https://the-university-of-north-carolina-at-charlotte.shoplightspeed.com/late-2020-13-inch-macbook-air-apple-m1-chip-with-8.html This ticket will be updated if the user responds or if we are able to test IGB on the new M1 Mac.
            Hide
            nfreese Nowlan Freese added a comment -

            The user reports that IGB 9.1.8 crashes on the M1 Mac. We will need to see if we can replicate the issue once we have an M1 Mac available to test.

            Show
            nfreese Nowlan Freese added a comment - The user reports that IGB 9.1.8 crashes on the M1 Mac. We will need to see if we can replicate the issue once we have an M1 Mac available to test.
            Hide
            ann.loraine Ann Loraine added a comment -

            There's a release of JDK8 for MacOS M1 chip that is available from Oracle.

            See: https://www.oracle.com/java/technologies/javase/jdk8-arm-downloads.html

            Ideas for what to try next:

            • See if Install4J company is making an M1-compatible JDK available (since it would probably already be tested)
            • Add the JDK to the Docker image
            • While we're updating the Docker image, upgrade Install4J as well?
            • Build an installer with this M1-compatible JDK
            • Ask our user (see above) to try running it on the M1 Mac
            Show
            ann.loraine Ann Loraine added a comment - There's a release of JDK8 for MacOS M1 chip that is available from Oracle. See: https://www.oracle.com/java/technologies/javase/jdk8-arm-downloads.html Ideas for what to try next: See if Install4J company is making an M1-compatible JDK available (since it would probably already be tested) Add the JDK to the Docker image While we're updating the Docker image, upgrade Install4J as well? Build an installer with this M1-compatible JDK Ask our user (see above) to try running it on the M1 Mac
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Install4J current version: 9
            IGB Docker image version: 8

            Install4J9 claims to have dual binaries that will allow us to build one single installer that works on Macs with Intel or M1 chips:

            install4j can now produce universal binaries for macOS to support Intel and Apple Silicon at the same time. In the media wizard, you can select the "Universal binaries" architecture on the "Installation options" step.

            from: https://www.ej-technologies.com/products/install4j/whatsnew9.html

            From detailed release notes:

            • Universal binaries architecture selection in the "Installation options" step of the macOS media wizards. Launchers then work with both x64 and aarch64 (Apple Silicon) architectures.
            • Universal JRE bundle generation on macOS. If the Universal binaries architecture is selected, the generated JRE bundle will include universal binaries for both x64 and aarch64 if the selected JDK release contains those architectures.

            Commencing effort to make a new Docker image with Install4J 9.

            Show
            ann.loraine Ann Loraine added a comment - - edited Install4J current version: 9 IGB Docker image version: 8 Install4J9 claims to have dual binaries that will allow us to build one single installer that works on Macs with Intel or M1 chips: install4j can now produce universal binaries for macOS to support Intel and Apple Silicon at the same time. In the media wizard, you can select the "Universal binaries" architecture on the "Installation options" step. from: https://www.ej-technologies.com/products/install4j/whatsnew9.html From detailed release notes: Universal binaries architecture selection in the "Installation options" step of the macOS media wizards. Launchers then work with both x64 and aarch64 (Apple Silicon) architectures. Universal JRE bundle generation on macOS. If the Universal binaries architecture is selected, the generated JRE bundle will include universal binaries for both x64 and aarch64 if the selected JDK release contains those architectures. Commencing effort to make a new Docker image with Install4J 9.
            Hide
            nfreese Nowlan Freese added a comment - - edited

            Additional user has reached out to say that IGB is crashing on their M1 Max Mac:

            I’ve tried to use version 9.1.8 in the past couple of days and it is super unstable – just crashes out of the blue. I’m running Monterey 12.3.1 on a MacBook Pro M1 Max if that info helps. Also none of the tabs in the upper ribbon work so to load a file I have to use the button with the file pic on it. I’ve attached a crash report. Please let me know if you have a fix. Obviously I can us UCSC or IGV but I really like your browser’s visualization so much better. Makes much prettier figures!

            Crash report attached as JavaApplicationStub-2022-04-28-072227.ips

            Show
            nfreese Nowlan Freese added a comment - - edited Additional user has reached out to say that IGB is crashing on their M1 Max Mac: I’ve tried to use version 9.1.8 in the past couple of days and it is super unstable – just crashes out of the blue. I’m running Monterey 12.3.1 on a MacBook Pro M1 Max if that info helps. Also none of the tabs in the upper ribbon work so to load a file I have to use the button with the file pic on it. I’ve attached a crash report. Please let me know if you have a fix. Obviously I can us UCSC or IGV but I really like your browser’s visualization so much better. Makes much prettier figures! Crash report attached as JavaApplicationStub-2022-04-28-072227.ips
            Hide
            ann.loraine Ann Loraine added a comment -

            The best course of action is to upgrade Install4J to include JREs for the new architecture, ideally a JRE that can work for both. For the next steps, I need to review the latest features for Install4J and make sure I know how to use them. For example, maven support appears to be improved quite a bit.

            I am going to close this ticket and create a new one for upgrading Install4J to version 9.

            cc: Nowlan Freese

            Show
            ann.loraine Ann Loraine added a comment - The best course of action is to upgrade Install4J to include JREs for the new architecture, ideally a JRE that can work for both. For the next steps, I need to review the latest features for Install4J and make sure I know how to use them. For example, maven support appears to be improved quite a bit. I am going to close this ticket and create a new one for upgrading Install4J to version 9. cc: Nowlan Freese
            Hide
            nfreese Nowlan Freese added a comment - - edited

            Additional user issue:

            I have macOS Monterey version 12.3.1 installed on my iMac. I tried reinstalling and deinstalling the IGB browser but Java is always crashing. In safe mode it is not the case. I was in contact with Apple and they recommended to get in contact with the developer.
            Are you aware of this issue?

            No, its not using one of the new apple M1 chips ( I attached a screenshot of the OS and the MacBook version).
            This is what I tried so far:

            • shut down and restart the Mac
              -Updating MacOS
              de and reinstalling IGB
              de de and reinstalling JAVA
            • running IGB in macOS safe mode (worked)
            • running IGB with another user (did not work)
            Show
            nfreese Nowlan Freese added a comment - - edited Additional user issue: I have macOS Monterey version 12.3.1 installed on my iMac. I tried reinstalling and deinstalling the IGB browser but Java is always crashing. In safe mode it is not the case. I was in contact with Apple and they recommended to get in contact with the developer. Are you aware of this issue? No, its not using one of the new apple M1 chips ( I attached a screenshot of the OS and the MacBook version). This is what I tried so far: shut down and restart the Mac -Updating MacOS de and reinstalling IGB de de and reinstalling JAVA running IGB in macOS safe mode (worked) running IGB with another user (did not work)
            Hide
            nfreese Nowlan Freese added a comment -

            The common thread for all three users that were having issues with IGB was the update to Monterey 12.3.1 on their Mac computers. Two of the users had M1 machines (M1 pro and M1 Max) while the third reported that their Mac did not have an M1 processor (assume it was an Intel). This would indicate to me that there is an issue with the 12.3.1 update and not a compatibility issue with M1 Macs.

            Show
            nfreese Nowlan Freese added a comment - The common thread for all three users that were having issues with IGB was the update to Monterey 12.3.1 on their Mac computers. Two of the users had M1 machines (M1 pro and M1 Max) while the third reported that their Mac did not have an M1 processor (assume it was an Intel). This would indicate to me that there is an issue with the 12.3.1 update and not a compatibility issue with M1 Macs.
            Hide
            nfreese Nowlan Freese added a comment -

            The new version of IGB (zulu) appears to have fixed the issues a user was experiencing:

            As of today, the IGB of the new version did not crash anymore.

            I guess it might continue to be OK. Just let you know this and thank you for your help.

            Show
            nfreese Nowlan Freese added a comment - The new version of IGB (zulu) appears to have fixed the issues a user was experiencing: As of today, the IGB of the new version did not crash anymore. I guess it might continue to be OK. Just let you know this and thank you for your help.

              People

              • Assignee:
                nfreese Nowlan Freese
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                2 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: