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Re: [mat-dev] java.io.FileNotFoundException: /mat-work/nikhil/MAT1.11/mat/../../sacbay-m-big77GB.inbound.index3096.log (Too many open files)
Hi Andrew,Kevin,

I am not able to modify the ulimit beyond 4096.

I tried the below command and got an exception.

[opc@ci-iad-mat-lab-01 ~]$ ulimit -n 90000

-bash: ulimit: open files: cannot modify limit: Operation not permitted


Here is ulimit command output

[opc@ci-iad-mat-lab-01 mat]$ ulimit -a

core file size          (blocks, -c) 0

data seg size           (kbytes, -d) unlimited

scheduling priority             (-e) 0

file size               (blocks, -f) unlimited

pending signals                 (-i) 239754

max locked memory       (kbytes, -l) 64

max memory size         (kbytes, -m) unlimited

open files                      (-n) 4096

pipe size            (512 bytes, -p) 8

POSIX message queues     (bytes, -q) 819200

real-time priority              (-r) 0

stack size              (kbytes, -s) 8192

cpu time               (seconds, -t) unlimited

max user processes              (-u) 4096

virtual memory          (kbytes, -v) unlimited

file locks                      (-x) unlimited




Regards

Nikhil Dongre


On Mon, Jul 12, 2021 at 11:43 PM Nikhil Dongre <nikhil.vilas@xxxxxxxxx> wrote:
Hi Andrew,

I think this is a very genuine scenario with 70GB + hprof files with MAT 1.11 as by default Linux os max support 4096 open files. 

And in our case 4089 (sacbay-m-big77GB.inbound.index4089.log) files I can see on my disk.

Once we started using MAT 1.11 it started falling for large hprof files 
and in our scenario we are processing upto 100GB files with old MAT 1.8 it was very very slow but rarely failed 

And if we think of the above solution, is there any way to calculate the on the basis of hprof file size? (Reason: upto 50GB hprof files we didn't face any issue and we may need to process max 100GB file) 

"It might cause performance or memory problems for other people if we reduced the number and so increased the size of the open temporary index files."

I agree with the above comment.

But is there any way to make this working for Large Heap Dumps.

Regards
Nikhil Dongre


On Fri, Jul 9, 2021 at 1:32 PM Andrew Johnson <andrew_johnson@xxxxxxxxxx> wrote:
Nikhil,

The code for this is here:
https://git.eclipse.org/r/plugins/gitiles/mat/org.eclipse.mat/+/refs/tags/R_1.12.0/plugins/org.eclipse.mat.parser/src/org/eclipse/mat/parser/index/IndexWriter.java

I think the current code is a reasonable compromise - I think it has one inbound.indexNNNN.log file for every 500,000 identifiers, so for the maximum possible 2^31 identifiers it could allocate 4295 files.

There are suggestions on the Internet that you can change the number of open files when starting a container:
https://docs.docker.com/engine/reference/commandline/run/#set-ulimits-in-container---ulimit
https://mtyurt.net/post/docker-how-to-increase-number-of-open-files-limit.html
E.g. $ docker run --ulimit nofile=1024:1024 --rm debian sh -c "ulimit -n"

It might cause performance or memory problems for other people if we reduced the number and so increased the size of the open temporary index files.

Regards,

Andrew Johnson






From:        "Nikhil Dongre" <nikhil.vilas@xxxxxxxxx>
To:        "Memory Analyzer Dev list" <mat-dev@xxxxxxxxxxx>
Date:        07/07/2021 17:56
Subject:        [EXTERNAL] Re: [mat-dev] java.io.FileNotFoundException: /mat-work/nikhil/MAT1.11/mat/../../sacbay-m-big77GB.inbound.index3096.log (Too many open files)
Sent by:        "mat-dev" <mat-dev-bounces@xxxxxxxxxxx>

Hi Andrew,

Thanks for quick work around.

But we have scenarios where we may not be able to change the limit as its container based solution. Once Hprof files are processed and HTML reports are generated the container will vanish and throughout we will not have access to the container.
And another scenario is hprof file size it may vary from 1gb to 100gb so fixing at OS level may not be the right solution. 

Please suggest.

Regards
Nikhil Dongre 

On Wed, Jul 7, 2021 at 5:09 PM Andrew Johnson <andrew_johnson@xxxxxxxxxx> wrote:
Memory Analyzer does create a lot of files at the re-indexing stage as it helps to build the inbound index. These are deleted once that stage is over, so you don't normally notice them.

You need to increase the limit on the number of open files for your process. Something like
ulimit -S -n 4096
would increase the soft limit for the process - if 4096 is too small for MAT with this dump you will still get the error. There is a hard limit of the number of open files:
ulimit -H -n
and an ordinary user can't increase the soft limit beyond the hard limit. If you need more then you need root access or a system administrator to increase the limits for your userid
The administrator might need to change something like the following.

/etc/security/limits.conf
* - nofile 16384

Once that is done you might need to log in again and run
ulimit -S -n 16384

Andrew Johnson




From:        "Nikhil Dongre" <nikhil.vilas@xxxxxxxxx>
To:        "Memory Analyzer Dev list" <mat-dev@xxxxxxxxxxx>
Date:        07/07/2021 06:51
Subject:        Re: [mat-dev] java.io.FileNotFoundException: /mat-work/nikhil/MAT1.11/mat/../../sacbay-m-big77GB.inbound.index3096.log (Too many open files)
Sent by:        "mat-dev" <mat-dev-bounces@xxxxxxxxxxx>

Here are some more details 
Please find the command ulimit -a output below :

[opc@ci-iad-mat-lab-01 mat]$ ulimit -a

core file size          (blocks, -c) 0

data seg size           (kbytes, -d) unlimited

scheduling priority             (-e) 0

file size               (blocks, -f) unlimited

pending signals                 (-i) 239754

max locked memory       (kbytes, -l) 64

max memory size         (kbytes, -m) unlimited

open files                      (-n) 1024

pipe size            (512 bytes, -p) 8

POSIX message queues     (bytes, -q) 819200

real-time priority              (-r) 0

stack size              (kbytes, -s) 8192

cpu time               (seconds, -t) unlimited

max user processes              (-u) 4096

virtual memory          (kbytes, -v) unlimited

file locks                      (-x) unlimited

[opc@ci-iad-mat-lab-01 mat]$ 

Hprof file size is : 77GB

MAT version : 1.11

And its failing after this step  "Re-indexing outbound index"

[Task: Parsing /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.hprof

[

Subtask: Scanning /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.hprof

[....................

[INFO] Wrote threads call stacks to /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.threads

[....................

[INFO] Heap /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.hprof contains 1,168,946,725 objects

[....................

Subtask: Extracting objects from /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.hprof

[................................................................................Task: Removing unreachable objects

[

Subtask: Searching for unreachable objects

[

Subtask: Marking reachable objects

[.

Subtask: Re-indexing objects

[.

[INFO] Removed 72,901,319 unreachable objects using 6,692,864,976 bytes

[..

Subtask: Re-indexing classes

[...

Subtask: Writing /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.idx.index

[....

Subtask: Writing /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.o2c.index

[.....

Subtask: Writing /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.a2s.index

[......

Subtask: Re-indexing outbound index

[......]

eclipse.buildId=unknown

java.version=1.8.0_292

java.vendor=Red Hat, Inc.

BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US

Framework arguments:  -application org.eclipse.mat.api.parse -DhprofStrictnessWarning=true ../../sacbay-m-big77GB.hprof org.eclipse.mat.api:suspects org.eclipse.mat.api:top_components org.eclipse.mat.api:overview

Command-line arguments:  -os linux -ws gtk -arch x86_64 -consolelog -application org.eclipse.mat.api.parse -DhprofStrictnessWarning=true ../../sacbay-m-big77GB.hprof org.eclipse.mat.api:suspects org.eclipse.mat.api:top_components org.eclipse.mat.api:overview

!ENTRY org.eclipse.osgi 4 0 2021-07-07 05:32:46.312

!MESSAGE Application error

!STACK 1

org.eclipse.mat.SnapshotException: Error opening heap dump 'sacbay-m-big77GB.hprof'. Check the error log for further details.

at org.eclipse.mat.parser.internal.SnapshotFactoryImpl.parse(SnapshotFactoryImpl.java:331)

at org.eclipse.mat.parser.internal.SnapshotFactoryImpl.openSnapshot(SnapshotFactoryImpl.java:167)

at org.eclipse.mat.snapshot.SnapshotFactory.openSnapshot(SnapshotFactory.java:147)

at org.eclipse.mat.internal.apps.ParseSnapshotApp.parse(ParseSnapshotApp.java:138)

at org.eclipse.mat.internal.apps.ParseSnapshotApp.start(ParseSnapshotApp.java:110)

at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)

at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:137)

at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:107)

at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)

at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:255)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:657)

at org.eclipse.equinox.launcher.Main.basicRun(Main.java:594)

at org.eclipse.equinox.launcher.Main.run(Main.java:1447)

at org.eclipse.equinox.launcher.Main.main(Main.java:1420)

Caused by: java.io.FileNotFoundException: /mat-work/nikhil/MAT1.11_Normal/mat/../../sacbay-m-big77GB.inbound.index3096.log (Too many open files)

at java.io.FileOutputStream.open0(Native Method)

at java.io.FileOutputStream.open(FileOutputStream.java:270)

at java.io.FileOutputStream.<init>(FileOutputStream.java:213)

at java.io.FileOutputStream.<init>(FileOutputStream.java:162)

at org.eclipse.mat.parser.index.IndexWriter$InboundWriter.log(IndexWriter.java:1237)

at org.eclipse.mat.parser.internal.GarbageCleaner.clean(GarbageCleaner.java:360)

at org.eclipse.mat.parser.internal.SnapshotFactoryImpl.parse(SnapshotFactoryImpl.java:282)

... 17 more



On Wed, Jul 7, 2021 at 9:03 AM Nikhil Dongre <nikhil.vilas@xxxxxxxxx> wrote:
Hi Kevin,

Thanks for the quick response.

Please find the command output below :

[opc@ci-iad-mat-lab-01 mat]$ ulimit -a

core file size          (blocks, -c) 0

data seg size           (kbytes, -d) unlimited

scheduling priority             (-e) 0

file size               (blocks, -f) unlimited

pending signals                 (-i) 239754

max locked memory       (kbytes, -l) 64

max memory size         (kbytes, -m) unlimited

open files                      (-n) 1024

pipe size            (512 bytes, -p) 8

POSIX message queues     (bytes, -q) 819200

real-time priority              (-r) 0

stack size              (kbytes, -s) 8192

cpu time               (seconds, -t) unlimited

max user processes              (-u) 4096

virtual memory          (kbytes, -v) unlimited

file locks                      (-x) unlimited

[opc@ci-iad-mat-lab-01 mat]$ 

Regards

Nikhil Dongre



On Wed, Jul 7, 2021 at 8:52 AM Kevin Grigorenko <kevin.grigorenko@xxxxxxxxxx> wrote:
The error "Too many open files" may occur because your file ulimit is too small, system-wide limits have been exceeded, or there is a bug in MAT creating too many file descriptors (in decreasing order of probability). Please start a terminal and send the output of the following command:

$ ulimit -a

--
Kevin Grigorenko
IBM App Platform SWAT




From:        "Nikhil Dongre" <nikhil.vilas@xxxxxxxxx>
To:        mat-dev@xxxxxxxxxxx
Date:        07/06/2021 06:01 PM
Subject:        [EXTERNAL] [mat-dev] java.io.FileNotFoundException: /mat-work/nikhil/MAT1.11/mat/../../sacbay-m-big77GB.inbound.index3096.log (Too many open files)
Sent by:        "mat-dev" <mat-dev-bounces@xxxxxxxxxxx>




Hi Team, When i tried to process process gz hprof file i got this exception  org.eclipse.mat.SnapshotException: Error opening heap dump 'sacbay-m-big77GB.hprof.gz'. Check the error log for further details. at org.eclipse.mat.parser.internal.SnapshotFactoryImpl.parse(SnapshotFactoryImpl.java:331)
Hi Team,

When i tried to process process gz hprof file i got this exception 

org.eclipse.mat.SnapshotException: Error opening heap dump 'sacbay-m-big77GB.hprof.gz'. Check the error log for further details.

at org.eclipse.mat.parser.internal.SnapshotFactoryImpl.parse(SnapshotFactoryImpl.java:331)

at org.eclipse.mat.parser.internal.SnapshotFactoryImpl.openSnapshot(SnapshotFactoryImpl.java:167)

at org.eclipse.mat.snapshot.SnapshotFactory.openSnapshot(SnapshotFactory.java:147)

at org.eclipse.mat.internal.apps.ParseSnapshotApp.parse(ParseSnapshotApp.java:138)

at org.eclipse.mat.internal.apps.ParseSnapshotApp.start(ParseSnapshotApp.java:110)

at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)

at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:137)

at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:107)

at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)

at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:255)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:657)

at org.eclipse.equinox.launcher.Main.basicRun(Main.java:594)

at org.eclipse.equinox.launcher.Main.run(Main.java:1447)

at org.eclipse.equinox.launcher.Main.main(Main.java:1420)

Caused by: java.io.FileNotFoundException: /mat-work/nikhil/MAT1.11/mat/../../sacbay-m-big77GB.inbound.index3096.log (Too many open files)

at java.io.FileOutputStream.open0(Native Method)

at java.io.FileOutputStream.open(FileOutputStream.java:270)

at java.io.FileOutputStream.<init>(FileOutputStream.java:213)

at java.io.FileOutputStream.<init>(FileOutputStream.java:162)

at org.eclipse.mat.parser.index.IndexWriter$InboundWriter.log(IndexWriter.java:1237)

at org.eclipse.mat.parser.internal.GarbageCleaner.clean(GarbageCleaner.java:360)

at org.eclipse.mat.parser.internal.SnapshotFactoryImpl.parse(SnapshotFactoryImpl.java:282)

... 17 more

MemoryAnalyzer:

An error has occurred. See the log file_______________________________________________
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_______________________________________________
mat-dev mailing list
mat-dev@xxxxxxxxxxx
To unsubscribe from this list, visit https://www.eclipse.org/mailman/listinfo/mat-dev_______________________________________________
mat-dev mailing list
mat-dev@xxxxxxxxxxx
To unsubscribe from this list, visit https://www.eclipse.org/mailman/listinfo/mat-dev



Unless stated otherwise above:
IBM United Kingdom Limited - Registered in England and Wales with number 741598.
Registered office: PO Box 41, North Harbour, Portsmouth, Hampshire PO6 3AU
_______________________________________________
mat-dev mailing list
mat-dev@xxxxxxxxxxx
To unsubscribe from this list, visit https://www.eclipse.org/mailman/listinfo/mat-dev_______________________________________________
mat-dev mailing list
mat-dev@xxxxxxxxxxx
To unsubscribe from this list, visit https://www.eclipse.org/mailman/listinfo/mat-dev



Unless stated otherwise above:
IBM United Kingdom Limited - Registered in England and Wales with number 741598.
Registered office: PO Box 41, North Harbour, Portsmouth, Hampshire PO6 3AU
 _______________________________________________
mat-dev mailing list
mat-dev@xxxxxxxxxxx
To unsubscribe from this list, visit https://www.eclipse.org/mailman/listinfo/mat-dev

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