MarvinSketch 5.4 for Mac OS takes a long time to open

MarvinSketch 5.4.0.1 for the Mac OS takes a long time to open. Is this a known issue? If so, is there a fix for it? Thank you.

I reinstalled JChem/Marvin 5.4.0.1 and this seemed to fix the problem. The applications now launch relatively quickly.

Interesting... so you say that when only Marvin was installed, it started slowly, but when you installed JChem on the top of it, it solved the problem? We will investigate this issue.

I spoke too soon. I reinstalled JChem/Marvin 5.4.0.1 under Mac OS 10.6.6. Immediately after reinstalling, Marvin Sketch opened relatively quickly. However, subsequent launches of the program have been extremely slow. If Marvin Sketch is launched and then closed, it opens again quickly, but if it is a "fresh" launch, it takes a long time.

There are two other items that might be related:

1. If the Marvin Sketch icon is placed in the Dock, when Marvin Sketch is opened and then closed, the icon in the Dock does not show a little arrow indicating that the program is still available in memory (like other programs do).

2. I installed Marvin Beans by installing JChem. However, the Marvin Beans installer does not start automatically if I select the option to run the Marvin Beans installer. Instead, I have to find the dmg file and start the installation from there. In contrast, the Windows Marvin Beans installer starts automatically from the JChem installation.

Thank you.

Thank you for the further info. We will try to reproduce it.

Best regards,

Akos

2. I installed Marvin Beans by installing JChem. However, the Marvin Beans installer does not start automatically if I select the option to run the Marvin Beans installer. Instead, I have to find the dmg file and start the installation from there. In contrast, the Windows Marvin Beans installer starts automatically from the JChem installation.

The auto launch of Marvin installer in OS X installer of JChem has not been implemented yet.
We have a task about that in our issue tracking system.

akospapp wrote:

Interesting... so you say that when only Marvin was installed, it started slowly, but when you installed JChem on the top of it, it solved the problem? We will investigate this issue.

To clarify: No, I installed the full JChem package that includes MarvinBeans, etc. Initially, I thought that reinstalling everything had solved the problem of MarvinSketch taking a long time to open, but the apparent solution was only temporary. It has reverted to taking a long time to open. If it finally opens, then subsequent openings are quicker, but again, this is temporary.

Have you tried launching MarvinSketch by the shell script (<MARVINHOME>/bin/msketch)?

Is it also slow?

I had not tried this previously, but I tried your suggestion. I changed
directory to:

/Applications/ChemAxon/MarvinBeans/bin

Then I ran ./msketch

MarvinSketch 5.4 eventually opened, but it took about 34 seconds.

Launching MarvinSketch either in the GUI or from the terminal takes a long
time the first time it is launched. However, if the application is closed,
it can be reopened within about 4 seconds. Nevertheless, if one waits for a
longer time, the system reverts to a very slow opening.

I have tried uninstalling/reinstalling JChem and MarvinBeans, but to no
avail. I have also repaired disk permissions, but this had no effect.

I look forward to your solution to this problem.

Thank you.

Rudy

I looked at the i4jlauncher.config file. It indicates problems with Java; however, Mac OS X (10.6.6) does not seem to permit installation of one's own Java, because Apple (thus far) provides its own Java. I have attached the i4jlauncher.config file as a zipped txt file for your inspection. If there is a way that I can repair Java in the Mac OS, please let me know. Thank you. --Rudy

Thanks for info.

If both shell script and install4j launcher for MarvinSketch are slow, it means that the problem is somewhere else than in the installer.

Probably, the JVM startup time is long. Is this problem also occurs with other Java applications?

Tamas:

I am not sure what other apps I have that run on Java. However, the problem is not localized to only one machine. I am having the same problem with MarvinSketch on another Mac machine. The machine is a different vintage, but it is running the same version of the Mac OS (10.6.6) and the same version of Java, provided by Apple (java version "1.6.0_22"; Java(TM) SE Runtime Environment (build 1.6.0_22-b04-307-10M3261); Java HotSpot(TM) Client VM (build 17.1-b03-307, mixed mode).

This is not a problem on my Windows machines running WinXP Pro. The Java version on my Windows machines is 1.6.0_23, Java SE runtime environment (build 1.6.0_23-b05); Java hotspot client VM (build 19.0-b09, mixed mode, sharing).

Thus, it appears that Windows is running a more recent version of Java, but this in itself might not explain the reasons that the Mac machines are having problems with running this particular Java app. In any event, it would be good if Apple would provide a Java update.

Thank you.

--Rudy

 

Tamas:

I have another app on the Mac that I believe runs under Java; it is Bioclipse 2.4. It launches in about 10 seconds; on the same machine, MarvinSketch takes about 70 seconds to launch.

--Rudy

Java VMs are totally different under OS X and Windows. Meanwhile Oracle implemented Java for Windows, Mac machines uses Apple own Java implementations. Of course, the Apple is compatible with the Oracle one. But there are some platform specific packages in the Apple version.

Thanks for the info.

We are checking it what can cause the slow startup time under OS X.

I installed JChem/Marvin Beans 5.4.1.1 on a new mac mini running OS 10.6.6. Marvin Sketch still takes a long time to open. Sometimes it will not open at all or it will take several attempts. It will eventually open after several minutes. I am not having this problem with the Windows version (Java).

We are still investigate it.