Received: by 10.42.132.5 with SMTP id b5mr4477849ict.7.1347897099736; Mon, 17 Sep 2012 08:51:39 -0700 (PDT) X-BeenThere: cytoscape-discuss@googlegroups.com Received: by 10.231.82.148 with SMTP id b20ls14559003ibl.9.gmail; Mon, 17 Sep 2012 08:51:37 -0700 (PDT) Received: by 10.42.90.4 with SMTP id i4mr4653515icm.19.1347897097229; Mon, 17 Sep 2012 08:51:37 -0700 (PDT) Received: by 10.42.90.4 with SMTP id i4mr4653514icm.19.1347897097206; Mon, 17 Sep 2012 08:51:37 -0700 (PDT) Return-Path: Received: from mail-ie0-f176.google.com (mail-ie0-f176.google.com [209.85.223.176]) by gmr-mx.google.com with ESMTPS id xd1si2680106igb.1.2012.09.17.08.51.37 (version=TLSv1/SSLv3 cipher=OTHER); Mon, 17 Sep 2012 08:51:37 -0700 (PDT) Received-SPF: pass (google.com: domain of hauld...@gmail.com designates 209.85.223.176 as permitted sender) client-ip=209.85.223.176; Authentication-Results: gmr-mx.google.com; spf=pass (google.com: domain of hauld...@gmail.com designates 209.85.223.176 as permitted sender) smtp.mail=hauld...@gmail.com; dkim=pass header...@gmail.com Received: by iecs9 with SMTP id s9so12346782iec.21 for ; Mon, 17 Sep 2012 08:51:37 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=4K4i/QvPbxGMXzmu0mb8tORWyDpR3JoVJOrGCKN3oBA=; b=XeWSW0e2UsQL8M5hDwIg/TU0PYxIKuL7wqVG78knZ8k7Dy/yLhqVhO4CUSymrOolyy PofwT5baNft/Rof5iQ/G8flVKYy7jeHiPRNSR9Tj53Hz+8x7hQQ/xa8y+AHqbjpLnMTi 48p2EfyjX/CqdEr+hC3viYFkJrOrI4fugRuUKRreQvS8btjTSzLkK5tPLUMuZcBOW0m2 M1wQJAD91+AhOgkkvzskHwVzlFd6eAI8Qbt/mUu184+CCmRHRAo3EjloHi4iPs70Ykwx Y1CEEa0YCId/QDI6KbVhWg1Uj5y/fLXxw9xX/skFSn1uIVm4vPas6H9EmScIJtKKtSRq grQA== MIME-Version: 1.0 Received: by 10.42.89.1 with SMTP id e1mr9325533icm.8.1347897097029; Mon, 17 Sep 2012 08:51:37 -0700 (PDT) Received: by 10.50.50.2 with HTTP; Mon, 17 Sep 2012 08:51:36 -0700 (PDT) In-Reply-To: References: <7108c567-9232-4efb-a8aa-f1e5c270c7fb@googlegroups.com> <9825d50f-fbc3-4977-94b0-975db26d40cb@googlegroups.com> Date: Mon, 17 Sep 2012 22:51:36 +0700 Message-ID: Subject: Re: [Cytoscape-discuss] Re: error when running cytoscape 3.0 From: "Duc-Hau, Le" To: cytoscape-discuss@googlegroups.com Content-Type: multipart/alternative; boundary=90e6ba3fceeda9897004c9e7bfcd --90e6ba3fceeda9897004c9e7bfcd Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thank you, Jason, It may be a particular limitation of Cy 3.0? Because it run OK if I set greater than 1200MB for maximum heap size (e.g,. -Xmx1600M) when I run Cy 2.8.x (I am using the same PC and win7, 32bit, 3G RAM for both Cy 3.0 and Cy 2.8.x). Cheers, Duc-Hau On Mon, Sep 17, 2012 at 10:05 PM, Jason Montojo wrote: > Hi Duc-Hau, > > That's a limitation of the 32-bit Java JVM. I can't run it with a heap > size greater than 1200M on my particular configuration. If you need acce= ss > to more memory, running 64-bit Java on a 64-bit OS is probably the best > solution. > > Hope this helps, > Jason > > > On Sat, Sep 15, 2012 at 12:08 AM, Duc-Hau, Le wrote: > >> Hi All, >> >> Regarding to the Cy 3.0 starting error (particularly, I am using Cy3.0 M= 6 >> version), I met another problem about maximum heap memory. That is if I = set >> JAVA_MAX_MEM greater than ~1000M, then it could not start and produced a= n >> error about Outofmemory (Even I installed 3GB RAM in my computer, I am n= ow >> using win7, 32 bit). However, it started perfectly with JAVA_MAX_MEM les= s >> than or equal to ~1000M. This will be a big problem if I run some plugin= s >> (after Cy 3.0 started) which require larger memory space. >> >> Any help will be appreciated >> >> Thanks, >> >> On Sat, Sep 15, 2012 at 12:35 AM, girishanem wrote= : >> >>> Hi Xuan-Hung, >>> >>> I also faced the same issue. For the first time execute cytoscape.bat. >>> If it fails try to execute karaf.bat( in my app environment its path is >>> Cy_3_1\target\framework\bin\karaf.bat). It will start the Cytoscape. An= d as >>> Jason said check your available RAM when you are executing Cytoscape.ba= t. >>> >>> Regards, >>> Girish Anem >>> >>> >>> On Wednesday, 12 September 2012 09:19:33 UTC+5:30, Xuan-Hung wrote: >>>> >>>> Hi all, >>>> After extracting it and run cytoscape.bat file in Windows 7, 32bit, an >>>> following error occurred: >>>> >>>> I already installed jdk_7u6. >>>> >>>> Please help to fix the Cytoscape 3.0 running problem. >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "cytoscape-discuss" group. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msg/cytoscape-discuss/-/ijfRmHBAPQ4J. >>> >>> To post to this group, send email to cytoscape-discuss@googlegroups.com= . >>> To unsubscribe from this group, send email to >>> cytoscape-discuss+unsubscribe@googlegroups.com. >>> For more options, visit this group at >>> http://groups.google.com/group/cytoscape-discuss?hl=3Den. >>> >> >> >> >> -- >> Duc-Hau Le, Ph.D (Vietnamese: L=C3=AA =C4=90=E1=BB=A9c H=E1=BA=ADu) >> Cell phone: (84) 912-324564 (Vietnam), (82)10-6869-2999 (Republic of >> Korea) >> Email:hauld...@gmail.com, hauld...@wru.vn >> Website: https://sites.google.com/site/duchaule2011/ >> Faculty of Computer Science and Engineering, Water Resources University. >> 175 Tay Son, Dong Da, Hanoi, Vietnam. >> >> -- >> You received this message because you are subscribed to the Google Group= s >> "cytoscape-discuss" group. >> To post to this group, send email to cytoscape-discuss@googlegroups.com. >> To unsubscribe from this group, send email to >> cytoscape-discuss+unsubscribe@googlegroups.com. >> For more options, visit this group at >> http://groups.google.com/group/cytoscape-discuss?hl=3Den. >> > > -- > You received this message because you are subscribed to the Google Groups > "cytoscape-discuss" group. > To post to this group, send email to cytoscape-discuss@googlegroups.com. > To unsubscribe from this group, send email to > cytoscape-discuss+unsubscribe@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/cytoscape-discuss?hl=3Den. > --=20 Duc-Hau Le, Ph.D (Vietnamese: L=C3=AA =C4=90=E1=BB=A9c H=E1=BA=ADu) Cell phone: (84) 912-324564 (Vietnam), (82)10-6869-2999 (Republic of Korea) Email:hauld...@gmail.com, hauld...@wru.vn Website: https://sites.google.com/site/duchaule2011/ Faculty of Computer Science and Engineering, Water Resources University. 175 Tay Son, Dong Da, Hanoi, Vietnam. --90e6ba3fceeda9897004c9e7bfcd Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thank you, Jason,

It may be a particular limitation of C= y 3.0? Because it run OK if I set greater than 1200MB for maximum heap size= (e.g,. -Xmx1600M) when I run Cy 2.8.x (I am using the same PC and win7, 32= bit, 3G RAM for both Cy 3.0 and Cy 2.8.x).

Cheers,
Duc-Hau

On Mon, Sep 17, 2012 at 10:05 PM, Jason Montojo <= jrr...@gmail.com&= gt; wrote:
Hi Duc-Hau,

That's a = limitation of the 32-bit Java JVM. =C2=A0I can't run it with a heap siz= e greater than 1200M on my particular configuration. =C2=A0If you need acce= ss to more memory, running 64-bit Java on a 64-bit OS is probably the best = solution.

Hope this helps,
Jason
=

On Sat, Sep 15, 2012 at 12:08 AM, Duc-Ha= u, Le <hauld...@gmail.com> wrote:
Hi All,

Regarding to the Cy 3.0 start= ing error (particularly, I am using Cy3.0 M6 version), I met another proble= m about maximum heap memory. That is if I set JAVA_MAX_MEM greater than ~10= 00M, then it could not start and produced an error about Outofmemory (Even = I installed 3GB RAM in my computer, I am now using win7, 32 bit). However, = it started perfectly with JAVA_MAX_MEM less than or equal to ~1000M. This w= ill be a big problem if I run some plugins (after Cy 3.0 started) which req= uire larger memory space.

Any help will be appreciated

Thanks,=C2=A0=C2=A0
<= br>
On Sat, Sep 15, 2012 at 12:35 AM, girishanem = <girisha...@gmail.com> wrote:
Hi Xuan-Hung,

I also face= d the same issue. For the first time execute cytoscape.bat. If it fails try= to execute karaf.bat( in my app environment its path is Cy_3_1\target\fram= ework\bin\karaf.bat). It will start the Cytoscape. And as Jason said check = your available RAM when you are executing Cytoscape.bat.

Regards,
Girish Anem


O= n Wednesday, 12 September 2012 09:19:33 UTC+5:30, Xuan-Hung wrote: Hi all,
After extracting it and run=C2=A0cytoscape.bat file in Windows 7= , 32bit,=C2=A0an following error occurred:
3D""
I already i= nstalled jdk_7u6.

Please help to fix the Cytoscape 3.0 running probl= em.

--
You received this message because you are subscribed to the Google Groups &= quot;cytoscape-discuss" group.
To view this discussion on the web visit https://groups= .google.com/d/msg/cytoscape-discuss/-/ijfRmHBAPQ4J.

=20 To post to this group, send email to cytoscape-discuss@googlegroups.com. To unsubscribe from this group, send email to cytoscape-discuss+= unsubscribe@googlegroups.com.
For more options, visit this group at http://groups.google.com/= group/cytoscape-discuss?hl=3Den.



= --
Duc-Hau Le, Ph.D (Vietnamese: L=C3=AA = =C4=90=E1=BB=A9c H=E1=BA=ADu)
Cell phone: (84) 912-324564 (Vietnam),=C2= =A0(82)10-6869-2999 (Republic of Korea)
Email:hauldhut@gmai= l.com,=C2=A0hauld...@wru.vn
Website: https://sites.google.com/site/duchaule2011/
Faculty of Compu= ter Science and Engineering, Water Resources University.
17= 5 Tay Son, Dong Da, Hanoi, Vietnam.

--
You received this message because you are subscribed to the Google Groups &= quot;cytoscape-discuss" group.
To post to this group, send email to cytoscape-discuss@googlegroups.com. To unsubscribe from this group, send email to cytoscape-discuss+= unsubscribe@googlegroups.com.
For more options, visit this group at http://groups.google.com/= group/cytoscape-discuss?hl=3Den.

=

--
You received this message because you are subscribed to the Google Groups &= quot;cytoscape-discuss" group.
To post to this group, send email to cytoscape-discuss@googlegroups.com. To unsubscribe from this group, send email to cytoscape-discuss+= unsubscribe@googlegroups.com.
For more options, visit this group at http://groups.google.com/= group/cytoscape-discuss?hl=3Den.



--
= Duc-Hau Le, Ph.D (Vietnamese: L=C3=AA =C4=90=E1=BB=A9c H=E1=BA=ADu)Cell phone: (84) 912-324564 (Vietnam),=C2=A0(82)10-6869-2999 (Repu= blic of Korea)
Email:hauld...@gmail.com,=C2=A0hauld...@wru.vn
Website: https://sites.google.com/site/duchaule2011/
Faculty of Compu= ter Science and Engineering, Water Resources University.
17= 5 Tay Son, Dong Da, Hanoi, Vietnam.
--90e6ba3fceeda9897004c9e7bfcd--