Jalview uses too much memory

Hi,

I'm having a problem with jalview using up way too much memory. It seems
to have allocated about 3.5 GB, and uses 99% of it [1], even with no
windows open. I've tried installing 2.7 from the Ubuntu repositories,
the webstart version, and also the "install anywhere" version. In
addition, as per the linked screenshot, I have visual artifacts when
panning. This seems much worse in 2.7, as the "install anywhere" version
(2.8) appears to correct itself after a second or so. I guess this might
be related to the lack of memory available.

I've tried different java versions too (using the "install anywhere"
version of Jalview):

java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.6) (6b27-1.12.6-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10) (7u25-2.3.10-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

All have the same problem. I'm using Kubuntu 13.04.

Cheers,
Lee.

[1] http://i.imgur.com/Sq5KZx4.png

Oops. Forgot to reply all ! Response to Lee’s question below.

J.

···

---------- Forwarded message ----------
From: “Jim Procter” <foreveremain@gmail.com>
Date: Aug 2, 2013 12:34 PM
Subject: Re: [Jalview-discuss] Jalview uses too much memory
To: “Lee Yeoh” <iamadonut@berlin.com>
Cc:

Hello Lee.

Are you sure you aren’t looking at the virtual memory footprint ? Java requests a large amount of cache for its runtime environment heap.

See this stack overflow question for a detailed explanation:

http://stackoverflow.com/questions/561245/virtual-memory-usage-from-java-under-linux-too-much-memory-used

On Aug 2, 2013 9:36 AM, “Lee Yeoh” <iamadonut@berlin.com> wrote:

Hi,

I’m having a problem with jalview using up way too much memory. It seems
to have allocated about 3.5 GB, and uses 99% of it [1], even with no
windows open. I’ve tried installing 2.7 from the Ubuntu repositories,
the webstart version, and also the “install anywhere” version. In
addition, as per the linked screenshot, I have visual artifacts when
panning. This seems much worse in 2.7, as the “install anywhere” version
(2.8) appears to correct itself after a second or so. I guess this might
be related to the lack of memory available.

I’ve tried different java versions too (using the “install anywhere”
version of Jalview):

java version “1.7.0_25”
Java™ SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot™ 64-Bit Server VM (build 23.25-b01, mixed mode)

java version “1.6.0_27”
OpenJDK Runtime Environment (IcedTea6 1.12.6) (6b27-1.12.6-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

java version “1.7.0_25”
OpenJDK Runtime Environment (IcedTea 2.3.10) (7u25-2.3.10-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

All have the same problem. I’m using Kubuntu 13.04.

Cheers,
Lee.

[1] http://i.imgur.com/Sq5KZx4.png


Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Hi Jim,

I’m not sure. I’m using the internal values from within Jalview, as per the bottom left of the screenshot.

Cheers,
Lee.

···

On 02/08/13 20:35, Jim Procter wrote:

I think you might be misreading the values.

The figures are telling you that 99% of the memory is available. Not 99%
in use. Try loading/creating some multiple sequence alignments, you should
see the percentage number go down indicating you're using up some of your
free memory.

Hope this helps.

Chris

···

On 02/08/2013 12:20, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi Jim,

I'm not sure. I'm using the internal values from within Jalview, as per
the bottom left of the screenshot.

Cheers,
Lee.

On 02/08/13 20:35, Jim Procter wrote:

Oops. Forgot to reply all ! Response to Lee's question below.
J.
---------- Forwarded message ----------
From: "Jim Procter" <foreveremain@gmail.com>
Date: Aug 2, 2013 12:34 PM
Subject: Re: [Jalview-discuss] Jalview uses too much memory
To: "Lee Yeoh" <iamadonut@berlin.com>
Cc:

Hello Lee.
Are you sure you aren't looking at the virtual memory footprint ? Java
requests a large amount of cache for its runtime environment heap.
See this stack overflow question for a detailed explanation:
http://stackoverflow.com/questions/561245/virtual-memory-usage-from-java-u
nder-linux-too-much-memory-used

On Aug 2, 2013 9:36 AM, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi,

I'm having a problem with jalview using up way too much memory. It seems
to have allocated about 3.5 GB, and uses 99% of it [1], even with no
windows open. I've tried installing 2.7 from the Ubuntu repositories,
the webstart version, and also the "install anywhere" version. In
addition, as per the linked screenshot, I have visual artifacts when
panning. This seems much worse in 2.7, as the "install anywhere" version
(2.8) appears to correct itself after a second or so. I guess this might
be related to the lack of memory available.

I've tried different java versions too (using the "install anywhere"
version of Jalview):

java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.6)
(6b27-1.12.6-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10)
(7u25-2.3.10-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

All have the same problem. I'm using Kubuntu 13.04.

Cheers,
Lee.

[1]
http://i.imgur.com/Sq5KZx4.png
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.orghttp://www.compbio.dundee.ac.uk/mailman/listinf
o/jalview-discuss

The University of Dundee is a registered Scottish Charity, No: SC015096

Indeed. 99% free not 99% used!

Geoff.

···

On 02/08/2013 14:55, Christian Cole wrote:

I think you might be misreading the values.

The figures are telling you that 99% of the memory is available. Not 99%
in use. Try loading/creating some multiple sequence alignments, you should
see the percentage number go down indicating you're using up some of your
free memory.

Hope this helps.

Chris

On 02/08/2013 12:20, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi Jim,

I'm not sure. I'm using the internal values from within Jalview, as per
the bottom left of the screenshot.

Cheers,
Lee.

On 02/08/13 20:35, Jim Procter wrote:

Oops. Forgot to reply all ! Response to Lee's question below.
J.
---------- Forwarded message ----------
From: "Jim Procter" <foreveremain@gmail.com>
Date: Aug 2, 2013 12:34 PM
Subject: Re: [Jalview-discuss] Jalview uses too much memory
To: "Lee Yeoh" <iamadonut@berlin.com>
Cc:

Hello Lee.
Are you sure you aren't looking at the virtual memory footprint ? Java
requests a large amount of cache for its runtime environment heap.
See this stack overflow question for a detailed explanation:
http://stackoverflow.com/questions/561245/virtual-memory-usage-from-java-u
nder-linux-too-much-memory-used

On Aug 2, 2013 9:36 AM, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi,

I'm having a problem with jalview using up way too much memory. It seems
to have allocated about 3.5 GB, and uses 99% of it [1], even with no
windows open. I've tried installing 2.7 from the Ubuntu repositories,
the webstart version, and also the "install anywhere" version. In
addition, as per the linked screenshot, I have visual artifacts when
panning. This seems much worse in 2.7, as the "install anywhere" version
(2.8) appears to correct itself after a second or so. I guess this might
be related to the lack of memory available.

I've tried different java versions too (using the "install anywhere"
version of Jalview):

java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.6)
(6b27-1.12.6-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10)
(7u25-2.3.10-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

All have the same problem. I'm using Kubuntu 13.04.

Cheers,
Lee.

[1]
http://i.imgur.com/Sq5KZx4.png
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.orghttp://www.compbio.dundee.ac.uk/mailman/listinf
o/jalview-discuss

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
Geoff Barton Professor of Bioinformatics
Head of Division of Computational Biology College of Life Sciences
University of Dundee, Scotland, UK. g.j.barton@dundee.ac.uk
Tel:+44 1382 385860 www.compbio.dundee.ac.uk

The University of Dundee is registered Scottish charity: No.SC015096

Ah. Ok. That was silly of me. Thanks for the answers.

There is also the issue of the visual garbage on scrolling? As I
mentioned, this seems much better in 2.8 (the "install anywhere"
version) as opposed to the 2.7 (Ubuntu repository version). I'm not sure
if this means the bug has been (somewhat) addressed? I'd prefer to use
repository versions generally, so they stay updated.

Cheers,
Lee.

···

On 03/08/13 00:00, Geoff Barton wrote:

Indeed. 99% free not 99% used!

Geoff.

On 02/08/2013 14:55, Christian Cole wrote:

I think you might be misreading the values.

The figures are telling you that 99% of the memory is available. Not 99%
in use. Try loading/creating some multiple sequence alignments, you should
see the percentage number go down indicating you're using up some of your
free memory.

Hope this helps.

Chris

On 02/08/2013 12:20, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi Jim,

I'm not sure. I'm using the internal values from within Jalview, as per
the bottom left of the screenshot.

Cheers,
Lee.

On 02/08/13 20:35, Jim Procter wrote:

Oops. Forgot to reply all ! Response to Lee's question below.
J.
---------- Forwarded message ----------
From: "Jim Procter" <foreveremain@gmail.com>
Date: Aug 2, 2013 12:34 PM
Subject: Re: [Jalview-discuss] Jalview uses too much memory
To: "Lee Yeoh" <iamadonut@berlin.com>
Cc:

Hello Lee.
Are you sure you aren't looking at the virtual memory footprint ? Java
requests a large amount of cache for its runtime environment heap.
See this stack overflow question for a detailed explanation:
http://stackoverflow.com/questions/561245/virtual-memory-usage-from-java-u
nder-linux-too-much-memory-used

On Aug 2, 2013 9:36 AM, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi,

I'm having a problem with jalview using up way too much memory. It seems
to have allocated about 3.5 GB, and uses 99% of it [1], even with no
windows open. I've tried installing 2.7 from the Ubuntu repositories,
the webstart version, and also the "install anywhere" version. In
addition, as per the linked screenshot, I have visual artifacts when
panning. This seems much worse in 2.7, as the "install anywhere" version
(2.8) appears to correct itself after a second or so. I guess this might
be related to the lack of memory available.

I've tried different java versions too (using the "install anywhere"
version of Jalview):

java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.6)
(6b27-1.12.6-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10)
(7u25-2.3.10-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

All have the same problem. I'm using Kubuntu 13.04.

Cheers,
Lee.

[1]
http://i.imgur.com/Sq5KZx4.png
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.orghttp://www.compbio.dundee.ac.uk/mailman/listinf
o/jalview-discuss

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Okay, I think I've tracked this down to a java bug. I can reproduce it
with either OpenJDK version, but scrolling is fine with Sun Java.

Thanks for all your help. Cheers,
Lee.

···

On 03/08/13 10:29, Lee Yeoh wrote:

Ah. Ok. That was silly of me. Thanks for the answers.

There is also the issue of the visual garbage on scrolling? As I
mentioned, this seems much better in 2.8 (the "install anywhere"
version) as opposed to the 2.7 (Ubuntu repository version). I'm not sure
if this means the bug has been (somewhat) addressed? I'd prefer to use
repository versions generally, so they stay updated.

Cheers,
Lee.

On 03/08/13 00:00, Geoff Barton wrote:

Indeed. 99% free not 99% used!

Geoff.

On 02/08/2013 14:55, Christian Cole wrote:

I think you might be misreading the values.

The figures are telling you that 99% of the memory is available. Not 99%
in use. Try loading/creating some multiple sequence alignments, you should
see the percentage number go down indicating you're using up some of your
free memory.

Hope this helps.

Chris

On 02/08/2013 12:20, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi Jim,

I'm not sure. I'm using the internal values from within Jalview, as per
the bottom left of the screenshot.

Cheers,
Lee.

On 02/08/13 20:35, Jim Procter wrote:

Oops. Forgot to reply all ! Response to Lee's question below.
J.
---------- Forwarded message ----------
From: "Jim Procter" <foreveremain@gmail.com>
Date: Aug 2, 2013 12:34 PM
Subject: Re: [Jalview-discuss] Jalview uses too much memory
To: "Lee Yeoh" <iamadonut@berlin.com>
Cc:

Hello Lee.
Are you sure you aren't looking at the virtual memory footprint ? Java
requests a large amount of cache for its runtime environment heap.
See this stack overflow question for a detailed explanation:
http://stackoverflow.com/questions/561245/virtual-memory-usage-from-java-u
nder-linux-too-much-memory-used

On Aug 2, 2013 9:36 AM, "Lee Yeoh" <iamadonut@berlin.com> wrote:

Hi,

I'm having a problem with jalview using up way too much memory. It seems
to have allocated about 3.5 GB, and uses 99% of it [1], even with no
windows open. I've tried installing 2.7 from the Ubuntu repositories,
the webstart version, and also the "install anywhere" version. In
addition, as per the linked screenshot, I have visual artifacts when
panning. This seems much worse in 2.7, as the "install anywhere" version
(2.8) appears to correct itself after a second or so. I guess this might
be related to the lack of memory available.

I've tried different java versions too (using the "install anywhere"
version of Jalview):

java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.6)
(6b27-1.12.6-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10)
(7u25-2.3.10-1ubuntu0.13.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

All have the same problem. I'm using Kubuntu 13.04.

Cheers,
Lee.

[1]
http://i.imgur.com/Sq5KZx4.png
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.orghttp://www.compbio.dundee.ac.uk/mailman/listinf
o/jalview-discuss

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss