Dataset Error EDDTableFromERDDAP
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Samantha Ouertani - NOAA Affiliate
Jul 17, 2023, 2:37:25 PM7/17/23
to ERDDAP
Hi Roy and Bob,
I am hoping to link a tabular dataset from another ERDDAP using dataset type = EDDTableFromERDDAP. I was able to load the same dataset from the same ERDDAP on an internal (not public) instance of ERDDAP. However, something goes wrong when I repeat the same steps on the public erddap.
The error issued in log.txt:
This error also appears when I try to generate the xml chunk using GenerateDatasetsXml.sh, specifically after entering the ERDDAP url for EDDType = EDDTableFromErddap.
The chunk of datasets.xml that triggers an error:
<dataset type="EDDTableFromErddap" datasetID="OSMC_30day" active="true">
<!-- OSMC 90 day RT data -->
<sourceUrl>https://osmc.noaa.gov/erddap/tabledap/OSMC_30day</sourceUrl>
</dataset>
<!-- OSMC 90 day RT data -->
<sourceUrl>https://osmc.noaa.gov/erddap/tabledap/OSMC_30day</sourceUrl>
</dataset>
The above xml successfully loads in the OSMC dataset in the internal ERDDAP instance. The URL itself is valid and working.
Details of the live ERDDAP (failed):
erddap v2.23
java version 17.0.7
Details of the internal ERDDAP (successful):
erddap v2.23
java version 17.0.7
Do either of you know why my data ingestion causes a "Connection reset" error when the dataset's URL is valid and working?
Thank you in advance,
Sam
Roy Mendelssohn - NOAA Federal
Jul 17, 2023, 4:55:26 PM7/17/23
to Samantha Ouertani - NOAA Affiliate, ERDDAP
Hi Sam:
I just tried it and it works fine for me. I am at home, so I have no special access. I would suggest the following:
1. Try again. Perhaps you just happened to try when the site was inaccessible.
2. If step one fails, try reaching the site say in a browser on each machine or use wget or curl or whatever. See if there is any difference.
3. If there is a difference try running "nslookup osmc.noaa.gov" and see if the is a difference to how they are resolved.
The error message means just what it says, it couldn't reach that site from that server, and that is something you will have to resolve first.
HTH,
Roy
PS - Whenever possible do not send screen shots of messages and the like but copy and paste the messages as text. Thanks.
> On Jul 17, 2023, at 11:37 AM, 'Samantha Ouertani - NOAA Affiliate' via ERDDAP <erd...@googlegroups.com> wrote:
>
> Hi Roy and Bob,
>
> I am hoping to link a tabular dataset from another ERDDAP using dataset type = EDDTableFromERDDAP. I was able to load the same dataset from the same ERDDAP on an internal (not public) instance of ERDDAP. However, something goes wrong when I repeat the same steps on the public erddap.
>
> The error issued in log.txt:
> You received this message because you are subscribed to the Google Groups "ERDDAP" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to erddap+un...@googlegroups.com.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/erddap/5572eb43-739e-4e9f-aa05-843d0988df94n%40googlegroups.com.
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Men...@noaa.gov www: https://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
I just tried it and it works fine for me. I am at home, so I have no special access. I would suggest the following:
1. Try again. Perhaps you just happened to try when the site was inaccessible.
2. If step one fails, try reaching the site say in a browser on each machine or use wget or curl or whatever. See if there is any difference.
3. If there is a difference try running "nslookup osmc.noaa.gov" and see if the is a difference to how they are resolved.
The error message means just what it says, it couldn't reach that site from that server, and that is something you will have to resolve first.
HTH,
Roy
PS - Whenever possible do not send screen shots of messages and the like but copy and paste the messages as text. Thanks.
> On Jul 17, 2023, at 11:37 AM, 'Samantha Ouertani - NOAA Affiliate' via ERDDAP <erd...@googlegroups.com> wrote:
>
> Hi Roy and Bob,
>
> I am hoping to link a tabular dataset from another ERDDAP using dataset type = EDDTableFromERDDAP. I was able to load the same dataset from the same ERDDAP on an internal (not public) instance of ERDDAP. However, something goes wrong when I repeat the same steps on the public erddap.
>
> The error issued in log.txt:
> <Screen Shot 2023-07-17 at 2.18.43 PM.png>
> This error also appears when I try to generate the xml chunk using GenerateDatasetsXml.sh, specifically after entering the ERDDAP url for EDDType = EDDTableFromErddap.
>
> The chunk of datasets.xml that triggers an error:
> <dataset type="EDDTableFromErddap" datasetID="OSMC_30day" active="true">
> <!-- OSMC 90 day RT data -->
> <sourceUrl>https://osmc.noaa.gov/erddap/tabledap/OSMC_30day</sourceUrl>
> </dataset>
> The above xml successfully loads in the OSMC dataset in the internal ERDDAP instance. The URL itself is valid and working.
>
> Details of the live ERDDAP (failed):
> https://erddap.aoml.noaa.gov/gdp/erddap/info/index.html?page=1&itemsPerPage=1000
> erddap v2.23
> java version 17.0.7
>
> Details of the internal ERDDAP (successful):
> erddap v2.23
> java version 17.0.7
>
> Do either of you know why my data ingestion causes a "Connection reset" error when the dataset's URL is valid and working?
>
> Thank you in advance,
> Sam
>
> --
> This error also appears when I try to generate the xml chunk using GenerateDatasetsXml.sh, specifically after entering the ERDDAP url for EDDType = EDDTableFromErddap.
>
> The chunk of datasets.xml that triggers an error:
> <dataset type="EDDTableFromErddap" datasetID="OSMC_30day" active="true">
> <!-- OSMC 90 day RT data -->
> <sourceUrl>https://osmc.noaa.gov/erddap/tabledap/OSMC_30day</sourceUrl>
> </dataset>
> The above xml successfully loads in the OSMC dataset in the internal ERDDAP instance. The URL itself is valid and working.
>
> Details of the live ERDDAP (failed):
> https://erddap.aoml.noaa.gov/gdp/erddap/info/index.html?page=1&itemsPerPage=1000
> erddap v2.23
> java version 17.0.7
>
> Details of the internal ERDDAP (successful):
> erddap v2.23
> java version 17.0.7
>
> Do either of you know why my data ingestion causes a "Connection reset" error when the dataset's URL is valid and working?
>
> Thank you in advance,
> Sam
>
> You received this message because you are subscribed to the Google Groups "ERDDAP" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to erddap+un...@googlegroups.com.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/erddap/5572eb43-739e-4e9f-aa05-843d0988df94n%40googlegroups.com.
> <Screen Shot 2023-07-17 at 2.18.43 PM.png>
**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Men...@noaa.gov www: https://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
Message has been deleted
Roy Mendelssohn - NOAA Federal
Jul 28, 2023, 12:40:47 PM7/28/23
to Samantha Ouertani - NOAA Affiliate, ERDDAP
Hi Sam:
This is a case where the error message means exactly what it says - there wasn't enough free memory to launch the program. All that scripts does is:
> java -cp classes:../../../lib/servlet-api.jar:lib/* -Xms1000M -Xmx1000M gov.noaa.pfel.erddap.GenerateDatasetsXml "$@"
>
Note that it requires 1000M of free memory to run. You can look at your systems memory usage by using the "top" command, and see of you have that much free memory. If you do, just try running again, it may have been a temporary situation while say garbage collection is going on. If you don't have enough space, you should try to figure out what is using all the space and make adjustments. Or you can try decreasing the amount of space the script needs by editing the above, but truthfully I do not know the innards of that script to know if it really does need that much memory, so I would say so that as a last resort, and it may fail. the "top" will tell you how much memory is there to allocate.
HTH,
-Roy
> On Jul 26, 2023, at 2:25 PM, 'Samantha Ouertani - NOAA Affiliate' via ERDDAP <erd...@googlegroups.com> wrote:
>
> Hi Roy,
>
> Thank you for the suggestions, I have not had a chance to try them. I'm now getting a different error message when I try to startup GenerateDatasetsXml.sh. As soon as I hit enter after "bash GenerateDatasetsXml.sh", I receive the following error:
>
> [samantha.ouertani@erddapdata WEB-INF]$ bash GenerateDatasetsXml.sh
> OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00000000c1800000, 1048576000, 0) failed; error='Not enough space' (errno=12)
> #
> # There is insufficient memory for the Java Runtime Environment to continue.
> # Native memory allocation (mmap) failed to map 1048576000 bytes for committing reserved memory.
> # An error report file with more information is saved as:
> # /tmp/hs_err_pid483556.log
> CONTENTS OF ERROR LOG HIGHLIGHTED IN RED, BELOW
>
> [samantha.ouertani@erddapdata WEB-INF]$ cat /tmp/hs_err_pid483556.log
> #
> # There is insufficient memory for the Java Runtime Environment to continue.
> # Native memory allocation (mmap) failed to map 1048576000 bytes for committing reserved memory.
> # Possible reasons:
> # The system is out of physical RAM or swap space
> # The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap
> # Possible solutions:
> # Reduce memory load on the system
> # Increase physical memory or swap space
> # Check if swap backing store is full
> # Decrease Java heap size (-Xmx/-Xms)
> # Decrease number of Java threads
> # Decrease Java thread stack sizes (-Xss)
> # Set larger code cache with -XX:ReservedCodeCacheSize=
> # JVM is running with Unscaled Compressed Oops mode in which the Java heap is
> # placed in the first 4GB address space. The Java Heap base address is the
> # maximum limit for the native heap growth. Please use -XX:HeapBaseMinAddress
> # to set the Java Heap base and to place the Java Heap above 4GB virtual address.
> # This output file may be truncated or incomplete.
> #
> # Out of Memory Error (os_linux.cpp:2781), pid=483556, tid=483557
> #
> # JRE version: (17.0.7+7) (build )
> # Java VM: OpenJDK 64-Bit Server VM (17.0.7+7-LTS, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64)
> # Core dump will be written. Default location: Core dumps may be processed with "/usr/lib/systemd/systemd-coredump %P %u %g %s %t %c %h %e" (or dumping to /opt/tomcat1/webapps/erddap/WEB-INF/core.483556)
> #
>
> --------------- S U M M A R Y ------------
>
> Command Line: -Xms1000M -Xmx1000M gov.noaa.pfel.erddap.GenerateDatasetsXml
>
> Host: Intel(R) Xeon(R) Gold 6230R CPU @ 2.10GHz, 4 cores, 31G, Rocky Linux release 8.8 (Green Obsidian)
> Time: Tue Jul 25 16:12:38 2023 EDT elapsed time: 0.010798 seconds (0d 0h 0m 0s)
>
> --------------- T H R E A D ---------------
>
> Current thread (0x00007f3ad00271b0): JavaThread "Unknown thread" [_thread_in_vm, id=483557, stack(0x00007f3ad926d000,0x00007f3ad936e000)]
>
> Stack: [0x00007f3ad926d000,0x00007f3ad936e000], sp=0x00007f3ad936c3d0, free space=1020k
> Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
> V [libjvm.so+0xf74ac6] VMError::report_and_die(int, char const*, char const*, __va_list_tag*, Thread*, unsigned char*, void*, void*, char const*, int, unsigned long)+0x1a6
> V [libjvm.so+0xf757cf] VMError::report_and_die(Thread*, char const*, int, unsigned long, VMErrorType, char const*, __va_list_tag*)+0x2f
> V [libjvm.so+0x621d15] report_vm_out_of_memory(char const*, int, unsigned long, VMErrorType, char const*, ...)+0xf5
> V [libjvm.so+0xc28880] os::pd_commit_memory_or_exit(char*, unsigned long, unsigned long, bool, char const*)+0xe0
> V [libjvm.so+0xc219ce] os::commit_memory_or_exit(char*, unsigned long, unsigned long, bool, char const*)+0x2e
> V [libjvm.so+0x75ad0c] G1PageBasedVirtualSpace::commit(unsigned long, unsigned long)+0x17c
> V [libjvm.so+0x76f1f3] G1RegionsLargerThanCommitSizeMapper::commit_regions(unsigned int, unsigned long, WorkGang*)+0x183
> V [libjvm.so+0x7fb17d] HeapRegionManager::commit_regions(unsigned int, unsigned long, WorkGang*)+0x5d
> V [libjvm.so+0x7fc1d2] HeapRegionManager::expand(unsigned int, unsigned int, WorkGang*)+0x32
> V [libjvm.so+0x7fc3da] HeapRegionManager::expand_by(unsigned int, WorkGang*)+0x7a
> V [libjvm.so+0x712dd9] G1CollectedHeap::expand(unsigned long, WorkGang*, double*)+0xe9
> V [libjvm.so+0x713547] G1CollectedHeap::initialize()+0x6e7
> V [libjvm.so+0xf22f9f] universe_init()+0xdf
> V [libjvm.so+0x81d13a] init_globals()+0x3a
> V [libjvm.so+0xefacf9] Threads::create_vm(JavaVMInitArgs*, bool*)+0x289
> V [libjvm.so+0x8e0f44] JNI_CreateJavaVM+0x64
> C [libjli.so+0x8f7d] JavaMain+0x9d
> C [libjli.so+0xd3dd] ThreadJavaMain+0xd
>
>
> --------------- P R O C E S S ---------------
>
> Threads class SMR info:
> _java_thread_list=0x00007f3ad873ba00, length=0, elements={
> }
>
> Java Threads: ( => current thread )
>
> Other Threads:
> 0x00007f3ad00637a0 GCTaskThread "GC Thread#0" [stack: 0x00007f3ad4935000,0x00007f3ad4a35000] [id=483558]
> 0x00007f3ad006ca80 ConcurrentGCThread "G1 Main Marker" [stack: 0x00007f3ad4833000,0x00007f3ad4933000] [id=483559]
> 0x00007f3ad006d9e0 ConcurrentGCThread "G1 Conc#0" [stack: 0x00007f3ad4731000,0x00007f3ad4831000] [id=483560]
>
> [error occurred during error reporting (printing all threads), id 0xb, SIGSEGV (0xb) at pc=0x00007f3ad7899cb4]
>
> VM state: not at safepoint (not fully initialized)
>
> VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
> [0x00007f3ad0024540] Heap_lock - owner thread: 0x00007f3ad00271b0
>
> Heap address: 0x00000000c1800000, size: 1000 MB, Compressed Oops mode: 32-bit
>
> CDS archive(s) mapped at: [0x0000000000000000-0x0000000000000000-0x0000000000000000), size 0, SharedBaseAddress: 0x0000000800000000, ArchiveRelocationMode: 0.
> Narrow klass base: 0x0000000000000000, Narrow klass shift: 0, Narrow klass range: 0x0
>
> GC Precious Log:
> <Empty>
>
> Heap:
> garbage-first heap total 0K, used 0K [0x00000000c1800000, 0x0000000100000000)
> region size 1024K, 0 young (0K), 0 survivors (0K)
>
> [error occurred during error reporting (printing heap information), id 0xb, SIGSEGV (0xb) at pc=0x00007f3ad7e43a0e]
>
> GC Heap History (0 events):
> No events
>
> Dll operation events (1 events):
> Event: 0.005 Loaded shared library /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
>
> Deoptimization events (0 events):
> No events
>
> Classes unloaded (0 events):
> No events
>
> Classes redefined (0 events):
> No events
>
> Internal exceptions (0 events):
> No events
>
> VM Operations (0 events):
> No events
>
> Events (1 events):
> Event: 0.005 Protecting memory [0x00007f3ad926d000,0x00007f3ad9271000] with protection modes 0
>
>
> Dynamic libraries:
> 55863d278000-55863d279000 r-xp 00000000 fd:03 46194 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/bin/java
> 55863d479000-55863d47a000 r--p 00001000 fd:03 46194 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/bin/java
> 55863d47a000-55863d47b000 rw-p 00002000 fd:03 46194 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/bin/java
> 55863ef56000-55863ef9d000 rw-p 00000000 00:00 0 [heap]
> 7f3aa8000000-7f3aa8021000 rw-p 00000000 00:00 0
> 7f3aa8021000-7f3aac000000 ---p 00000000 00:00 0
> 7f3aac000000-7f3aac021000 rw-p 00000000 00:00 0
> 7f3aac021000-7f3ab0000000 ---p 00000000 00:00 0
> 7f3ab0000000-7f3ab0021000 rw-p 00000000 00:00 0
> 7f3ab0021000-7f3ab4000000 ---p 00000000 00:00 0
> 7f3ab539f000-7f3ab7fae000 rw-p 00000000 00:00 0
> 7f3ab7fae000-7f3ab8f4e000 ---p 00000000 00:00 0
> 7f3ab8f4e000-7f3ab91be000 rwxp 00000000 00:00 0
> 7f3ab91be000-7f3ac0485000 ---p 00000000 00:00 0
> 7f3ac0485000-7f3ac06f5000 rwxp 00000000 00:00 0
> 7f3ac06f5000-7f3ac0a16000 ---p 00000000 00:00 0
> 7f3ac0a16000-7f3ac0c86000 rwxp 00000000 00:00 0
> 7f3ac0c86000-7f3ac7f4e000 ---p 00000000 00:00 0
> 7f3ac7f4e000-7f3ad0000000 r--s 00000000 fd:03 33608284 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/modules
> 7f3ad0000000-7f3ad0091000 rw-p 00000000 00:00 0
> 7f3ad0091000-7f3ad4000000 ---p 00000000 00:00 0
> 7f3ad432b000-7f3ad472f000 rw-p 00000000 00:00 0
> 7f3ad472f000-7f3ad4730000 ---p 00000000 00:00 0
> 7f3ad4730000-7f3ad4831000 rw-p 00000000 00:00 0
> 7f3ad4831000-7f3ad4832000 ---p 00000000 00:00 0
> 7f3ad4832000-7f3ad4933000 rw-p 00000000 00:00 0
> 7f3ad4933000-7f3ad4934000 ---p 00000000 00:00 0
> 7f3ad4934000-7f3ad4a35000 rw-p 00000000 00:00 0
> 7f3ad4a35000-7f3ad5fb1000 ---p 00000000 00:00 0
> 7f3ad5fb1000-7f3ad63ba000 rw-p 00000000 00:00 0
> 7f3ad63ba000-7f3ad64a0000 ---p 00000000 00:00 0
> 7f3ad64a0000-7f3ad64a5000 rw-p 00000000 00:00 0
> 7f3ad64a5000-7f3ad658b000 ---p 00000000 00:00 0
> 7f3ad658b000-7f3ad65b0000 r-xp 00000000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad65b0000-7f3ad67b0000 ---p 00025000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad67b0000-7f3ad67b1000 r--p 00025000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad67b1000-7f3ad67b2000 rw-p 00026000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad67b2000-7f3ad67b3000 rw-p 00000000 00:00 0
> 7f3ad67b3000-7f3ad67be000 r-xp 00000000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad67be000-7f3ad69be000 ---p 0000b000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad69be000-7f3ad69bf000 r--p 0000b000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad69bf000-7f3ad69c0000 rw-p 0000c000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad69c0000-7f3ad69c6000 rw-p 00000000 00:00 0
> 7f3ad69c6000-7f3ad69e1000 r-xp 00000000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad69e1000-7f3ad6be1000 ---p 0001b000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad6be1000-7f3ad6be3000 r--p 0001b000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad6be3000-7f3ad6be4000 rw-p 0001d000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad6be4000-7f3ad6d64000 r-xp 00000000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6d64000-7f3ad6f64000 ---p 00180000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6f64000-7f3ad6f65000 r--p 00180000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6f65000-7f3ad6f66000 rw-p 00181000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6f66000-7f3ad6f6d000 r-xp 00000000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad6f6d000-7f3ad716c000 ---p 00007000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad716c000-7f3ad716d000 r--p 00006000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad716d000-7f3ad716e000 rw-p 00007000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad716e000-7f3ad83ff000 r-xp 00000000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad83ff000-7f3ad85fe000 ---p 01291000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad85fe000-7f3ad86b7000 r--p 01290000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad86b7000-7f3ad86ec000 rw-p 01349000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad86ec000-7f3ad8746000 rw-p 00000000 00:00 0
> 7f3ad8746000-7f3ad8901000 r-xp 00000000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8901000-7f3ad8b01000 ---p 001bb000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8b01000-7f3ad8b05000 r--p 001bb000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8b05000-7f3ad8b07000 rw-p 001bf000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8b07000-7f3ad8b0b000 rw-p 00000000 00:00 0
> 7f3ad8b0b000-7f3ad8b0e000 r-xp 00000000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8b0e000-7f3ad8d0d000 ---p 00003000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8d0d000-7f3ad8d0e000 r--p 00002000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8d0e000-7f3ad8d0f000 rw-p 00003000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8d0f000-7f3ad8d2a000 r-xp 00000000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8d2a000-7f3ad8f29000 ---p 0001b000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8f29000-7f3ad8f2a000 r--p 0001a000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8f2a000-7f3ad8f2b000 rw-p 0001b000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8f2b000-7f3ad8f2f000 rw-p 00000000 00:00 0
> 7f3ad8f2f000-7f3ad8f48000 r-xp 00000000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad8f48000-7f3ad9147000 ---p 00019000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad9147000-7f3ad9148000 r--p 00018000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad9148000-7f3ad9149000 rw-p 00019000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad9149000-7f3ad9177000 r-xp 00000000 fd:03 50335398 /usr/lib64/ld-2.28.so
> 7f3ad9237000-7f3ad925e000 rw-p 00000000 00:00 0
> 7f3ad925e000-7f3ad9265000 ---p 00000000 00:00 0
> 7f3ad9265000-7f3ad926d000 rw-s 00000000 fd:03 33606689 /tmp/hsperfdata_samantha.ouertani/483556
> 7f3ad926d000-7f3ad9271000 ---p 00000000 00:00 0
> 7f3ad9271000-7f3ad9370000 rw-p 00000000 00:00 0
> 7f3ad9372000-7f3ad9373000 ---p 00000000 00:00 0
> 7f3ad9373000-7f3ad9374000 r--p 00000000 00:00 0
> 7f3ad9374000-7f3ad9375000 ---p 00000000 00:00 0
> 7f3ad9375000-7f3ad9377000 rw-p 00000000 00:00 0
> 7f3ad9377000-7f3ad9378000 r--p 0002e000 fd:03 50335398 /usr/lib64/ld-2.28.so
> 7f3ad9378000-7f3ad937a000 rw-p 0002f000 fd:03 50335398 /usr/lib64/ld-2.28.so
> 7fff42b9d000-7fff42bbe000 rw-p 00000000 00:00 0 [stack]
> 7fff42bdf000-7fff42be3000 r--p 00000000 00:00 0 [vvar]
> 7fff42be3000-7fff42be5000 r-xp 00000000 00:00 0 [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
>
>
> VM Arguments:
> jvm_args: -Xms1000M -Xmx1000M
> java_command: gov.noaa.pfel.erddap.GenerateDatasetsXml
> java_class_path (initial): classes:../../../lib/servlet-api.jar:lib/animal-sniffer-annotations-1.22.jar:lib/annotations-2.20.9.jar:lib/annotations-4.1.1.4.jar:lib/apache-client-2.20.9.jar:lib/api-common-2.6.1.jar:lib/arns-2.20.9.jar:lib/asm-5.0.3.jar:lib/asm-analysis-5.0.3.jar:lib/asm-commons-5.0.3.jar:lib/asm-tree-5.0.3.jar:lib/asm-util-5.0.3.jar:lib/auth-2.20.9.jar:lib/auto-value-1.10.1.jar:lib/auto-value-annotations-1.10.1.jar:lib/aws-core-2.20.9.jar:lib/aws-crt-0.21.7.jar:lib/aws-query-protocol-2.20.9.jar:lib/aws-xml-protocol-2.20.9.jar:lib/cassandra-driver-core-3.11.3.jar:lib/checker-qual-3.5.0.jar:lib/commons-codec-1.15.jar:lib/commons-compress-1.22.jar:lib/commons-jexl3-3.2.1.jar:lib/commons-logging-1.2.jar:lib/conscrypt-openjdk-uber-2.5.2.jar:lib/endpoints-spi-2.20.9.jar:lib/error_prone_annotations-2.11.0.jar:lib/eventstream-1.0.1.jar:lib/failureaccess-1.0.1.jar:lib/gax-2.23.1.jar:lib/gax-grpc-2.23.1.jar:lib/gax-httpjson-0.108.1.jar:lib/google-api-client-2.2.0.jar:lib/google-api-services-translate-v2-rev20170525-2.0.0.jar:lib/google-auth-library-credentials-1.16.0.jar:lib/google-auth-library-oauth2-http-1.16.0.jar:lib/google-cloud-core-2.11.0.jar:lib/google-cloud-core-http-2.11.0.jar:lib/google-cloud-translate-2.11.0.jar:lib/google-http-client-1.42.3.jar:lib/google-http-client-apache-v2-1.42.3.jar:lib/google-http-client-appengine-1.42.3.jar:lib/google-http-client-gson-1.42.3.jar:lib/google-http-client-jackson2-1.42.3.jar:lib/google-oauth-client-1.34.1.jar:lib/grpc-alts-1.53.0.jar:lib/grpc-api-1.53.0.jar:lib/grpc-auth-1.53.0.jar:lib/grpc-context-1.53.0.jar:lib/grpc-core-1.53.0.jar:lib/grpc-googleapis-1.53.0.jar:lib/grpc-grpclb-1.53.0.jar:lib/grpc-netty-shaded-1.53.0.jar:lib/grpc-protobuf-1.53.0.jar:lib/grpc-protobuf-lite-1.53.0.jar:lib/grpc-services-1.53.0.jar:lib/grpc-stub-1.53.0.jar:lib/grpc-xds-1.53.0.jar:lib/gson-2.10.1.jar:lib/guava-31.1-jre.jar:lib/http-client-spi-2.20.9.jar:lib/httpclient-4.5.14.jar:lib/httpcore-4.4.16.jar:lib/itext-1.3.1.jar:lib/j2o
> Launcher Type: SUN_STANDARD
>
> [Global flags]
> intx CICompilerCount = 3 {product} {ergonomic}
> uint ConcGCThreads = 1 {product} {ergonomic}
> uint G1ConcRefinementThreads = 4 {product} {ergonomic}
> size_t G1HeapRegionSize = 1048576 {product} {ergonomic}
> uintx GCDrainStackTargetSize = 64 {product} {ergonomic}
> size_t InitialHeapSize = 1048576000 {product} {command line}
> size_t MarkStackSize = 4194304 {product} {ergonomic}
> size_t MaxHeapSize = 1048576000 {product} {command line}
> size_t MinHeapDeltaBytes = 1048576 {product} {ergonomic}
> size_t MinHeapSize = 1048576000 {product} {command line}
> uintx NonNMethodCodeHeapSize = 5832780 {pd product} {ergonomic}
> uintx NonProfiledCodeHeapSize = 122912730 {pd product} {ergonomic}
> uintx ProfiledCodeHeapSize = 122912730 {pd product} {ergonomic}
> uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic}
> bool SegmentedCodeCache = true {product} {ergonomic}
> size_t SoftMaxHeapSize = 1048576000 {manageable} {ergonomic}
> bool UseCompressedClassPointers = true {product lp64_product} {ergonomic}
> bool UseCompressedOops = true {product lp64_product} {ergonomic}
> bool UseG1GC = true {product} {ergonomic}
>
> Logging:
> Log output configuration:
> #0: stdout all=warning uptime,level,tags
> #1: stderr all=off uptime,level,tags
>
> Environment Variables:
> PATH=/home/samantha.ouertani/.local/bin:/home/samantha.ouertani/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
> SHELL=/bin/bash
> LANG=en_US.UTF-8
> TERM=vt100
>
> Active Locale:
> LC_ALL=C
> LC_COLLATE=C
> LC_CTYPE=C
> LC_MESSAGES=C
> LC_MONETARY=C
> LC_NUMERIC=C
> LC_TIME=C
>
> Signal Handlers:
> SIGSEGV: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGBUS: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGFPE: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGPIPE: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGXFSZ: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGILL: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGUSR2: SR_handler in libjvm.so, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGHUP: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked
> SIGINT: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked
> SIGTERM: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked
> SIGQUIT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGTRAP: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
>
>
> --------------- S Y S T E M ---------------
>
> OS:
> Rocky Linux release 8.8 (Green Obsidian)
> uname: Linux 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64
> OS uptime: 4 days 1:46 hours
> libc: glibc 2.28 NPTL 2.28
> rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/infinity , NPROC 127417/127417 , NOFILE 262144/262144 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK 64k/64k
> load average: 0.13 0.04 0.01
>
> /proc/meminfo:
> MemTotal: 32654412 kB
> MemFree: 267552 kB
> MemAvailable: 114652 kB
> Buffers: 0 kB
> Cached: 201584 kB
> SwapCached: 74176 kB
> Active: 25323656 kB
> Inactive: 6774556 kB
> Active(anon): 25217400 kB
> Inactive(anon): 6688580 kB
> Active(file): 106256 kB
> Inactive(file): 85976 kB
> Unevictable: 4420 kB
> Mlocked: 420 kB
> SwapTotal: 975868 kB
> SwapFree: 0 kB
> Dirty: 0 kB
> Writeback: 0 kB
> AnonPages: 31826548 kB
> Mapped: 56336 kB
> Shmem: 9456 kB
> KReclaimable: 39404 kB
> Slab: 89772 kB
> SReclaimable: 39404 kB
> SUnreclaim: 50368 kB
> KernelStack: 4448 kB
> PageTables: 71252 kB
> NFS_Unstable: 0 kB
> Bounce: 0 kB
> WritebackTmp: 0 kB
> CommitLimit: 17303072 kB
> Committed_AS: 36837096 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed: 73836 kB
> VmallocChunk: 0 kB
> Percpu: 1680 kB
> HardwareCorrupted: 0 kB
> AnonHugePages: 10211328 kB
> ShmemHugePages: 0 kB
> ShmemPmdMapped: 0 kB
> FileHugePages: 0 kB
> FilePmdMapped: 0 kB
> HugePages_Total: 0
> HugePages_Free: 0
> HugePages_Rsvd: 0
> HugePages_Surp: 0
> Hugepagesize: 2048 kB
> Hugetlb: 0 kB
> DirectMap4k: 294768 kB
> DirectMap2M: 19628032 kB
> DirectMap1G: 15728640 kB
>
> /sys/kernel/mm/transparent_hugepage/enabled: [always] madvise never
> /sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts parameter): always defer defer+madvise [madvise] never
>
> Process Memory:
> Virtual Size: 782716K (peak: 1794368K)
> Resident Set Size: 26592K (peak: 26592K) (anon: 14196K, file: 12396K, shmem: 0K)
> Swapped out: 0K
> C-Heap outstanding allocations: 21324K, retained: 527K
> glibc malloc tunables: (default)
>
> /proc/sys/kernel/threads-max (system-wide limit on the number of threads): 254834
> /proc/sys/vm/max_map_count (maximum number of memory map areas a process may have): 65530
> /proc/sys/kernel/pid_max (system-wide limit on number of process identifiers): 4194304
>
> container (cgroup) information:
> container_type: cgroupv1
> cpu_cpuset_cpus: 0-3
> cpu_memory_nodes: 0
> active_processor_count: 4
> cpu_quota: no quota
> cpu_period: 100000
> cpu_shares: no shares
> memory_limit_in_bytes: unlimited
> memory_and_swap_limit_in_bytes: unlimited
> memory_soft_limit_in_bytes: unlimited
> memory_usage_in_bytes: 49224 k
> memory_max_usage_in_bytes: 4011564 k
> kernel_memory_usage_in_bytes: 1896 k
> kernel_memory_max_usage_in_bytes: unlimited
> kernel_memory_limit_in_bytes: 3871660 k
> maximum number of tasks: 203867
> current number of tasks: 10
>
> KVM virtualization detected
> Steal ticks since vm start: 0
> Steal ticks percentage since vm start: 0.000
>
> CPU: total 4 (initial active 4) (1 cores per cpu, 1 threads per core) family 6 model 85 stepping 7 microcode 0x5003302, cx8, cmov, fxsr, mmx, 3dnowpref, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, lzcnt, tsc, avx, avx2, aes, erms, clmul, bmi1, bmi2, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, fma, vzeroupper, avx512_vnni, clflush, clflushopt, clwb, hv
> CPU Model and flags from /proc/cpuinfo:
> model name : Intel(R) Xeon(R) Gold 6230R CPU @ 2.10GHz
> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology cpuid tsc_known_freq pni pclmulqdq vmx ssse3 fma cx16 pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves arat umip pku ospke avx512_vnni md_clear arch_capabilities
>
> Online cpus: 0-3
> Offline cpus:
> BIOS frequency limitation: <Not Available>
> Frequency switch latency (ns): <Not Available>
> Available cpu frequencies: <Not Available>
> Current governor: <Not Available>
> Core performance/turbo boost: <Not Available>
>
> Memory: 4k page, physical 32654412k(274608k free), swap 975868k(0k free)
> Page Sizes: 4k
>
> vm_info: OpenJDK 64-Bit Server VM (17.0.7+7-LTS) for linux-amd64 JRE (17.0.7+7-LTS), built on May 16 2023 11:37:11 by "mockbuild" with gcc 8.5.0 20210514 (Red Hat 8.5.0-18)
>
> END.
> END OF LOG ERROR MESSAGE
>
> The tomcat JAVA_OPTs settings:
> JAVA_OPTS="$JAVA_OPTS -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -Doracle.jdbc.V8Compatible="true" -Djava.awt.headless=true -server -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xmx25g -Xms25g -XX:+HeapDumpOnOutOfMemoryError"
>
> ERDDAP status page:
> OS info: totalCPULoad=0.0068413615 processCPULoad=1.7713537E-4 totalMemory=31889MB freeMemory=1139MB totalSwapSpace=952MB freeSwapSpace=883MB Number of active requests=1 Number of threads: Tomcat-waiting=13, inotify=2, other=11 0 gc calls, 0 requests shed, and 0 dangerousMemoryEmails since last major LoadDatasets MemoryInUse= 78 MB (highWaterMark= 344 MB) (Xmx ~= 25600 MB)
>
> The VM hosting ERDDAP has 60 GB. I'm not sure where this "memory" issue is originating from. Can you help me please? The ERDDAP's two datasets are still accessible with no issues ( https://erddap.aoml.noaa.gov/gdp/erddap/status.html)
> To view this discussion on the web, visit https://groups.google.com/d/msgid/erddap/77adb468-f30c-4f6e-8270-39b726965f06n%40googlegroups.com.
This is a case where the error message means exactly what it says - there wasn't enough free memory to launch the program. All that scripts does is:
> java -cp classes:../../../lib/servlet-api.jar:lib/* -Xms1000M -Xmx1000M gov.noaa.pfel.erddap.GenerateDatasetsXml "$@"
>
Note that it requires 1000M of free memory to run. You can look at your systems memory usage by using the "top" command, and see of you have that much free memory. If you do, just try running again, it may have been a temporary situation while say garbage collection is going on. If you don't have enough space, you should try to figure out what is using all the space and make adjustments. Or you can try decreasing the amount of space the script needs by editing the above, but truthfully I do not know the innards of that script to know if it really does need that much memory, so I would say so that as a last resort, and it may fail. the "top" will tell you how much memory is there to allocate.
HTH,
-Roy
> On Jul 26, 2023, at 2:25 PM, 'Samantha Ouertani - NOAA Affiliate' via ERDDAP <erd...@googlegroups.com> wrote:
>
> Hi Roy,
>
> Thank you for the suggestions, I have not had a chance to try them. I'm now getting a different error message when I try to startup GenerateDatasetsXml.sh. As soon as I hit enter after "bash GenerateDatasetsXml.sh", I receive the following error:
>
> [samantha.ouertani@erddapdata WEB-INF]$ bash GenerateDatasetsXml.sh
> OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00000000c1800000, 1048576000, 0) failed; error='Not enough space' (errno=12)
> #
> # There is insufficient memory for the Java Runtime Environment to continue.
> # Native memory allocation (mmap) failed to map 1048576000 bytes for committing reserved memory.
> # An error report file with more information is saved as:
> # /tmp/hs_err_pid483556.log
> CONTENTS OF ERROR LOG HIGHLIGHTED IN RED, BELOW
>
> [samantha.ouertani@erddapdata WEB-INF]$ cat /tmp/hs_err_pid483556.log
> #
> # There is insufficient memory for the Java Runtime Environment to continue.
> # Native memory allocation (mmap) failed to map 1048576000 bytes for committing reserved memory.
> # Possible reasons:
> # The system is out of physical RAM or swap space
> # The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap
> # Possible solutions:
> # Reduce memory load on the system
> # Increase physical memory or swap space
> # Check if swap backing store is full
> # Decrease Java heap size (-Xmx/-Xms)
> # Decrease number of Java threads
> # Decrease Java thread stack sizes (-Xss)
> # Set larger code cache with -XX:ReservedCodeCacheSize=
> # JVM is running with Unscaled Compressed Oops mode in which the Java heap is
> # placed in the first 4GB address space. The Java Heap base address is the
> # maximum limit for the native heap growth. Please use -XX:HeapBaseMinAddress
> # to set the Java Heap base and to place the Java Heap above 4GB virtual address.
> # This output file may be truncated or incomplete.
> #
> # Out of Memory Error (os_linux.cpp:2781), pid=483556, tid=483557
> #
> # JRE version: (17.0.7+7) (build )
> # Java VM: OpenJDK 64-Bit Server VM (17.0.7+7-LTS, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64)
> # Core dump will be written. Default location: Core dumps may be processed with "/usr/lib/systemd/systemd-coredump %P %u %g %s %t %c %h %e" (or dumping to /opt/tomcat1/webapps/erddap/WEB-INF/core.483556)
> #
>
> --------------- S U M M A R Y ------------
>
> Command Line: -Xms1000M -Xmx1000M gov.noaa.pfel.erddap.GenerateDatasetsXml
>
> Host: Intel(R) Xeon(R) Gold 6230R CPU @ 2.10GHz, 4 cores, 31G, Rocky Linux release 8.8 (Green Obsidian)
> Time: Tue Jul 25 16:12:38 2023 EDT elapsed time: 0.010798 seconds (0d 0h 0m 0s)
>
> --------------- T H R E A D ---------------
>
> Current thread (0x00007f3ad00271b0): JavaThread "Unknown thread" [_thread_in_vm, id=483557, stack(0x00007f3ad926d000,0x00007f3ad936e000)]
>
> Stack: [0x00007f3ad926d000,0x00007f3ad936e000], sp=0x00007f3ad936c3d0, free space=1020k
> Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
> V [libjvm.so+0xf74ac6] VMError::report_and_die(int, char const*, char const*, __va_list_tag*, Thread*, unsigned char*, void*, void*, char const*, int, unsigned long)+0x1a6
> V [libjvm.so+0xf757cf] VMError::report_and_die(Thread*, char const*, int, unsigned long, VMErrorType, char const*, __va_list_tag*)+0x2f
> V [libjvm.so+0x621d15] report_vm_out_of_memory(char const*, int, unsigned long, VMErrorType, char const*, ...)+0xf5
> V [libjvm.so+0xc28880] os::pd_commit_memory_or_exit(char*, unsigned long, unsigned long, bool, char const*)+0xe0
> V [libjvm.so+0xc219ce] os::commit_memory_or_exit(char*, unsigned long, unsigned long, bool, char const*)+0x2e
> V [libjvm.so+0x75ad0c] G1PageBasedVirtualSpace::commit(unsigned long, unsigned long)+0x17c
> V [libjvm.so+0x76f1f3] G1RegionsLargerThanCommitSizeMapper::commit_regions(unsigned int, unsigned long, WorkGang*)+0x183
> V [libjvm.so+0x7fb17d] HeapRegionManager::commit_regions(unsigned int, unsigned long, WorkGang*)+0x5d
> V [libjvm.so+0x7fc1d2] HeapRegionManager::expand(unsigned int, unsigned int, WorkGang*)+0x32
> V [libjvm.so+0x7fc3da] HeapRegionManager::expand_by(unsigned int, WorkGang*)+0x7a
> V [libjvm.so+0x712dd9] G1CollectedHeap::expand(unsigned long, WorkGang*, double*)+0xe9
> V [libjvm.so+0x713547] G1CollectedHeap::initialize()+0x6e7
> V [libjvm.so+0xf22f9f] universe_init()+0xdf
> V [libjvm.so+0x81d13a] init_globals()+0x3a
> V [libjvm.so+0xefacf9] Threads::create_vm(JavaVMInitArgs*, bool*)+0x289
> V [libjvm.so+0x8e0f44] JNI_CreateJavaVM+0x64
> C [libjli.so+0x8f7d] JavaMain+0x9d
> C [libjli.so+0xd3dd] ThreadJavaMain+0xd
>
>
> --------------- P R O C E S S ---------------
>
> Threads class SMR info:
> _java_thread_list=0x00007f3ad873ba00, length=0, elements={
> }
>
> Java Threads: ( => current thread )
>
> Other Threads:
> 0x00007f3ad00637a0 GCTaskThread "GC Thread#0" [stack: 0x00007f3ad4935000,0x00007f3ad4a35000] [id=483558]
> 0x00007f3ad006ca80 ConcurrentGCThread "G1 Main Marker" [stack: 0x00007f3ad4833000,0x00007f3ad4933000] [id=483559]
> 0x00007f3ad006d9e0 ConcurrentGCThread "G1 Conc#0" [stack: 0x00007f3ad4731000,0x00007f3ad4831000] [id=483560]
>
> [error occurred during error reporting (printing all threads), id 0xb, SIGSEGV (0xb) at pc=0x00007f3ad7899cb4]
>
> VM state: not at safepoint (not fully initialized)
>
> VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
> [0x00007f3ad0024540] Heap_lock - owner thread: 0x00007f3ad00271b0
>
> Heap address: 0x00000000c1800000, size: 1000 MB, Compressed Oops mode: 32-bit
>
> CDS archive(s) mapped at: [0x0000000000000000-0x0000000000000000-0x0000000000000000), size 0, SharedBaseAddress: 0x0000000800000000, ArchiveRelocationMode: 0.
> Narrow klass base: 0x0000000000000000, Narrow klass shift: 0, Narrow klass range: 0x0
>
> GC Precious Log:
> <Empty>
>
> Heap:
> garbage-first heap total 0K, used 0K [0x00000000c1800000, 0x0000000100000000)
> region size 1024K, 0 young (0K), 0 survivors (0K)
>
> [error occurred during error reporting (printing heap information), id 0xb, SIGSEGV (0xb) at pc=0x00007f3ad7e43a0e]
>
> GC Heap History (0 events):
> No events
>
> Dll operation events (1 events):
> Event: 0.005 Loaded shared library /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
>
> Deoptimization events (0 events):
> No events
>
> Classes unloaded (0 events):
> No events
>
> Classes redefined (0 events):
> No events
>
> Internal exceptions (0 events):
> No events
>
> VM Operations (0 events):
> No events
>
> Events (1 events):
> Event: 0.005 Protecting memory [0x00007f3ad926d000,0x00007f3ad9271000] with protection modes 0
>
>
> Dynamic libraries:
> 55863d278000-55863d279000 r-xp 00000000 fd:03 46194 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/bin/java
> 55863d479000-55863d47a000 r--p 00001000 fd:03 46194 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/bin/java
> 55863d47a000-55863d47b000 rw-p 00002000 fd:03 46194 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/bin/java
> 55863ef56000-55863ef9d000 rw-p 00000000 00:00 0 [heap]
> 7f3aa8000000-7f3aa8021000 rw-p 00000000 00:00 0
> 7f3aa8021000-7f3aac000000 ---p 00000000 00:00 0
> 7f3aac000000-7f3aac021000 rw-p 00000000 00:00 0
> 7f3aac021000-7f3ab0000000 ---p 00000000 00:00 0
> 7f3ab0000000-7f3ab0021000 rw-p 00000000 00:00 0
> 7f3ab0021000-7f3ab4000000 ---p 00000000 00:00 0
> 7f3ab539f000-7f3ab7fae000 rw-p 00000000 00:00 0
> 7f3ab7fae000-7f3ab8f4e000 ---p 00000000 00:00 0
> 7f3ab8f4e000-7f3ab91be000 rwxp 00000000 00:00 0
> 7f3ab91be000-7f3ac0485000 ---p 00000000 00:00 0
> 7f3ac0485000-7f3ac06f5000 rwxp 00000000 00:00 0
> 7f3ac06f5000-7f3ac0a16000 ---p 00000000 00:00 0
> 7f3ac0a16000-7f3ac0c86000 rwxp 00000000 00:00 0
> 7f3ac0c86000-7f3ac7f4e000 ---p 00000000 00:00 0
> 7f3ac7f4e000-7f3ad0000000 r--s 00000000 fd:03 33608284 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/modules
> 7f3ad0000000-7f3ad0091000 rw-p 00000000 00:00 0
> 7f3ad0091000-7f3ad4000000 ---p 00000000 00:00 0
> 7f3ad432b000-7f3ad472f000 rw-p 00000000 00:00 0
> 7f3ad472f000-7f3ad4730000 ---p 00000000 00:00 0
> 7f3ad4730000-7f3ad4831000 rw-p 00000000 00:00 0
> 7f3ad4831000-7f3ad4832000 ---p 00000000 00:00 0
> 7f3ad4832000-7f3ad4933000 rw-p 00000000 00:00 0
> 7f3ad4933000-7f3ad4934000 ---p 00000000 00:00 0
> 7f3ad4934000-7f3ad4a35000 rw-p 00000000 00:00 0
> 7f3ad4a35000-7f3ad5fb1000 ---p 00000000 00:00 0
> 7f3ad5fb1000-7f3ad63ba000 rw-p 00000000 00:00 0
> 7f3ad63ba000-7f3ad64a0000 ---p 00000000 00:00 0
> 7f3ad64a0000-7f3ad64a5000 rw-p 00000000 00:00 0
> 7f3ad64a5000-7f3ad658b000 ---p 00000000 00:00 0
> 7f3ad658b000-7f3ad65b0000 r-xp 00000000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad65b0000-7f3ad67b0000 ---p 00025000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad67b0000-7f3ad67b1000 r--p 00025000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad67b1000-7f3ad67b2000 rw-p 00026000 fd:03 33608261 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjava.so
> 7f3ad67b2000-7f3ad67b3000 rw-p 00000000 00:00 0
> 7f3ad67b3000-7f3ad67be000 r-xp 00000000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad67be000-7f3ad69be000 ---p 0000b000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad69be000-7f3ad69bf000 r--p 0000b000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad69bf000-7f3ad69c0000 rw-p 0000c000 fd:03 50335417 /usr/lib64/libnss_files-2.28.so
> 7f3ad69c0000-7f3ad69c6000 rw-p 00000000 00:00 0
> 7f3ad69c6000-7f3ad69e1000 r-xp 00000000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad69e1000-7f3ad6be1000 ---p 0001b000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad6be1000-7f3ad6be3000 r--p 0001b000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad6be3000-7f3ad6be4000 rw-p 0001d000 fd:03 33608264 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjimage.so
> 7f3ad6be4000-7f3ad6d64000 r-xp 00000000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6d64000-7f3ad6f64000 ---p 00180000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6f64000-7f3ad6f65000 r--p 00180000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6f65000-7f3ad6f66000 rw-p 00181000 fd:03 50335409 /usr/lib64/libm-2.28.so
> 7f3ad6f66000-7f3ad6f6d000 r-xp 00000000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad6f6d000-7f3ad716c000 ---p 00007000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad716c000-7f3ad716d000 r--p 00006000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad716d000-7f3ad716e000 rw-p 00007000 fd:03 50335423 /usr/lib64/librt-2.28.so
> 7f3ad716e000-7f3ad83ff000 r-xp 00000000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad83ff000-7f3ad85fe000 ---p 01291000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad85fe000-7f3ad86b7000 r--p 01290000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad86b7000-7f3ad86ec000 rw-p 01349000 fd:03 17176826 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/server/libjvm.so
> 7f3ad86ec000-7f3ad8746000 rw-p 00000000 00:00 0
> 7f3ad8746000-7f3ad8901000 r-xp 00000000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8901000-7f3ad8b01000 ---p 001bb000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8b01000-7f3ad8b05000 r--p 001bb000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8b05000-7f3ad8b07000 rw-p 001bf000 fd:03 50335405 /usr/lib64/libc-2.28.so
> 7f3ad8b07000-7f3ad8b0b000 rw-p 00000000 00:00 0
> 7f3ad8b0b000-7f3ad8b0e000 r-xp 00000000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8b0e000-7f3ad8d0d000 ---p 00003000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8d0d000-7f3ad8d0e000 r--p 00002000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8d0e000-7f3ad8d0f000 rw-p 00003000 fd:03 50335407 /usr/lib64/libdl-2.28.so
> 7f3ad8d0f000-7f3ad8d2a000 r-xp 00000000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8d2a000-7f3ad8f29000 ---p 0001b000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8f29000-7f3ad8f2a000 r--p 0001a000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8f2a000-7f3ad8f2b000 rw-p 0001b000 fd:03 50335419 /usr/lib64/libpthread-2.28.so
> 7f3ad8f2b000-7f3ad8f2f000 rw-p 00000000 00:00 0
> 7f3ad8f2f000-7f3ad8f48000 r-xp 00000000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad8f48000-7f3ad9147000 ---p 00019000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad9147000-7f3ad9148000 r--p 00018000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad9148000-7f3ad9149000 rw-p 00019000 fd:03 33608265 /usr/lib/jvm/java-17-openjdk-17.0.7.0.7-3.el8.x86_64/lib/libjli.so
> 7f3ad9149000-7f3ad9177000 r-xp 00000000 fd:03 50335398 /usr/lib64/ld-2.28.so
> 7f3ad9237000-7f3ad925e000 rw-p 00000000 00:00 0
> 7f3ad925e000-7f3ad9265000 ---p 00000000 00:00 0
> 7f3ad9265000-7f3ad926d000 rw-s 00000000 fd:03 33606689 /tmp/hsperfdata_samantha.ouertani/483556
> 7f3ad926d000-7f3ad9271000 ---p 00000000 00:00 0
> 7f3ad9271000-7f3ad9370000 rw-p 00000000 00:00 0
> 7f3ad9372000-7f3ad9373000 ---p 00000000 00:00 0
> 7f3ad9373000-7f3ad9374000 r--p 00000000 00:00 0
> 7f3ad9374000-7f3ad9375000 ---p 00000000 00:00 0
> 7f3ad9375000-7f3ad9377000 rw-p 00000000 00:00 0
> 7f3ad9377000-7f3ad9378000 r--p 0002e000 fd:03 50335398 /usr/lib64/ld-2.28.so
> 7f3ad9378000-7f3ad937a000 rw-p 0002f000 fd:03 50335398 /usr/lib64/ld-2.28.so
> 7fff42b9d000-7fff42bbe000 rw-p 00000000 00:00 0 [stack]
> 7fff42bdf000-7fff42be3000 r--p 00000000 00:00 0 [vvar]
> 7fff42be3000-7fff42be5000 r-xp 00000000 00:00 0 [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
>
>
> VM Arguments:
> jvm_args: -Xms1000M -Xmx1000M
> java_command: gov.noaa.pfel.erddap.GenerateDatasetsXml
> java_class_path (initial): classes:../../../lib/servlet-api.jar:lib/animal-sniffer-annotations-1.22.jar:lib/annotations-2.20.9.jar:lib/annotations-4.1.1.4.jar:lib/apache-client-2.20.9.jar:lib/api-common-2.6.1.jar:lib/arns-2.20.9.jar:lib/asm-5.0.3.jar:lib/asm-analysis-5.0.3.jar:lib/asm-commons-5.0.3.jar:lib/asm-tree-5.0.3.jar:lib/asm-util-5.0.3.jar:lib/auth-2.20.9.jar:lib/auto-value-1.10.1.jar:lib/auto-value-annotations-1.10.1.jar:lib/aws-core-2.20.9.jar:lib/aws-crt-0.21.7.jar:lib/aws-query-protocol-2.20.9.jar:lib/aws-xml-protocol-2.20.9.jar:lib/cassandra-driver-core-3.11.3.jar:lib/checker-qual-3.5.0.jar:lib/commons-codec-1.15.jar:lib/commons-compress-1.22.jar:lib/commons-jexl3-3.2.1.jar:lib/commons-logging-1.2.jar:lib/conscrypt-openjdk-uber-2.5.2.jar:lib/endpoints-spi-2.20.9.jar:lib/error_prone_annotations-2.11.0.jar:lib/eventstream-1.0.1.jar:lib/failureaccess-1.0.1.jar:lib/gax-2.23.1.jar:lib/gax-grpc-2.23.1.jar:lib/gax-httpjson-0.108.1.jar:lib/google-api-client-2.2.0.jar:lib/google-api-services-translate-v2-rev20170525-2.0.0.jar:lib/google-auth-library-credentials-1.16.0.jar:lib/google-auth-library-oauth2-http-1.16.0.jar:lib/google-cloud-core-2.11.0.jar:lib/google-cloud-core-http-2.11.0.jar:lib/google-cloud-translate-2.11.0.jar:lib/google-http-client-1.42.3.jar:lib/google-http-client-apache-v2-1.42.3.jar:lib/google-http-client-appengine-1.42.3.jar:lib/google-http-client-gson-1.42.3.jar:lib/google-http-client-jackson2-1.42.3.jar:lib/google-oauth-client-1.34.1.jar:lib/grpc-alts-1.53.0.jar:lib/grpc-api-1.53.0.jar:lib/grpc-auth-1.53.0.jar:lib/grpc-context-1.53.0.jar:lib/grpc-core-1.53.0.jar:lib/grpc-googleapis-1.53.0.jar:lib/grpc-grpclb-1.53.0.jar:lib/grpc-netty-shaded-1.53.0.jar:lib/grpc-protobuf-1.53.0.jar:lib/grpc-protobuf-lite-1.53.0.jar:lib/grpc-services-1.53.0.jar:lib/grpc-stub-1.53.0.jar:lib/grpc-xds-1.53.0.jar:lib/gson-2.10.1.jar:lib/guava-31.1-jre.jar:lib/http-client-spi-2.20.9.jar:lib/httpclient-4.5.14.jar:lib/httpcore-4.4.16.jar:lib/itext-1.3.1.jar:lib/j2o
> Launcher Type: SUN_STANDARD
>
> [Global flags]
> intx CICompilerCount = 3 {product} {ergonomic}
> uint ConcGCThreads = 1 {product} {ergonomic}
> uint G1ConcRefinementThreads = 4 {product} {ergonomic}
> size_t G1HeapRegionSize = 1048576 {product} {ergonomic}
> uintx GCDrainStackTargetSize = 64 {product} {ergonomic}
> size_t InitialHeapSize = 1048576000 {product} {command line}
> size_t MarkStackSize = 4194304 {product} {ergonomic}
> size_t MaxHeapSize = 1048576000 {product} {command line}
> size_t MinHeapDeltaBytes = 1048576 {product} {ergonomic}
> size_t MinHeapSize = 1048576000 {product} {command line}
> uintx NonNMethodCodeHeapSize = 5832780 {pd product} {ergonomic}
> uintx NonProfiledCodeHeapSize = 122912730 {pd product} {ergonomic}
> uintx ProfiledCodeHeapSize = 122912730 {pd product} {ergonomic}
> uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic}
> bool SegmentedCodeCache = true {product} {ergonomic}
> size_t SoftMaxHeapSize = 1048576000 {manageable} {ergonomic}
> bool UseCompressedClassPointers = true {product lp64_product} {ergonomic}
> bool UseCompressedOops = true {product lp64_product} {ergonomic}
> bool UseG1GC = true {product} {ergonomic}
>
> Logging:
> Log output configuration:
> #0: stdout all=warning uptime,level,tags
> #1: stderr all=off uptime,level,tags
>
> Environment Variables:
> PATH=/home/samantha.ouertani/.local/bin:/home/samantha.ouertani/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
> SHELL=/bin/bash
> LANG=en_US.UTF-8
> TERM=vt100
>
> Active Locale:
> LC_ALL=C
> LC_COLLATE=C
> LC_CTYPE=C
> LC_MESSAGES=C
> LC_MONETARY=C
> LC_NUMERIC=C
> LC_TIME=C
>
> Signal Handlers:
> SIGSEGV: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGBUS: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGFPE: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGPIPE: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGXFSZ: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGILL: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
> SIGUSR2: SR_handler in libjvm.so, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGHUP: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked
> SIGINT: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked
> SIGTERM: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked
> SIGQUIT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked
> SIGTRAP: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked
>
>
> --------------- S Y S T E M ---------------
>
> OS:
> Rocky Linux release 8.8 (Green Obsidian)
> uname: Linux 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64
> OS uptime: 4 days 1:46 hours
> libc: glibc 2.28 NPTL 2.28
> rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/infinity , NPROC 127417/127417 , NOFILE 262144/262144 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK 64k/64k
> load average: 0.13 0.04 0.01
>
> /proc/meminfo:
> MemTotal: 32654412 kB
> MemFree: 267552 kB
> MemAvailable: 114652 kB
> Buffers: 0 kB
> Cached: 201584 kB
> SwapCached: 74176 kB
> Active: 25323656 kB
> Inactive: 6774556 kB
> Active(anon): 25217400 kB
> Inactive(anon): 6688580 kB
> Active(file): 106256 kB
> Inactive(file): 85976 kB
> Unevictable: 4420 kB
> Mlocked: 420 kB
> SwapTotal: 975868 kB
> SwapFree: 0 kB
> Dirty: 0 kB
> Writeback: 0 kB
> AnonPages: 31826548 kB
> Mapped: 56336 kB
> Shmem: 9456 kB
> KReclaimable: 39404 kB
> Slab: 89772 kB
> SReclaimable: 39404 kB
> SUnreclaim: 50368 kB
> KernelStack: 4448 kB
> PageTables: 71252 kB
> NFS_Unstable: 0 kB
> Bounce: 0 kB
> WritebackTmp: 0 kB
> CommitLimit: 17303072 kB
> Committed_AS: 36837096 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed: 73836 kB
> VmallocChunk: 0 kB
> Percpu: 1680 kB
> HardwareCorrupted: 0 kB
> AnonHugePages: 10211328 kB
> ShmemHugePages: 0 kB
> ShmemPmdMapped: 0 kB
> FileHugePages: 0 kB
> FilePmdMapped: 0 kB
> HugePages_Total: 0
> HugePages_Free: 0
> HugePages_Rsvd: 0
> HugePages_Surp: 0
> Hugepagesize: 2048 kB
> Hugetlb: 0 kB
> DirectMap4k: 294768 kB
> DirectMap2M: 19628032 kB
> DirectMap1G: 15728640 kB
>
> /sys/kernel/mm/transparent_hugepage/enabled: [always] madvise never
> /sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts parameter): always defer defer+madvise [madvise] never
>
> Process Memory:
> Virtual Size: 782716K (peak: 1794368K)
> Resident Set Size: 26592K (peak: 26592K) (anon: 14196K, file: 12396K, shmem: 0K)
> Swapped out: 0K
> C-Heap outstanding allocations: 21324K, retained: 527K
> glibc malloc tunables: (default)
>
> /proc/sys/kernel/threads-max (system-wide limit on the number of threads): 254834
> /proc/sys/vm/max_map_count (maximum number of memory map areas a process may have): 65530
> /proc/sys/kernel/pid_max (system-wide limit on number of process identifiers): 4194304
>
> container (cgroup) information:
> container_type: cgroupv1
> cpu_cpuset_cpus: 0-3
> cpu_memory_nodes: 0
> active_processor_count: 4
> cpu_quota: no quota
> cpu_period: 100000
> cpu_shares: no shares
> memory_limit_in_bytes: unlimited
> memory_and_swap_limit_in_bytes: unlimited
> memory_soft_limit_in_bytes: unlimited
> memory_usage_in_bytes: 49224 k
> memory_max_usage_in_bytes: 4011564 k
> kernel_memory_usage_in_bytes: 1896 k
> kernel_memory_max_usage_in_bytes: unlimited
> kernel_memory_limit_in_bytes: 3871660 k
> maximum number of tasks: 203867
> current number of tasks: 10
>
> KVM virtualization detected
> Steal ticks since vm start: 0
> Steal ticks percentage since vm start: 0.000
>
> CPU: total 4 (initial active 4) (1 cores per cpu, 1 threads per core) family 6 model 85 stepping 7 microcode 0x5003302, cx8, cmov, fxsr, mmx, 3dnowpref, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, lzcnt, tsc, avx, avx2, aes, erms, clmul, bmi1, bmi2, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, fma, vzeroupper, avx512_vnni, clflush, clflushopt, clwb, hv
> CPU Model and flags from /proc/cpuinfo:
> model name : Intel(R) Xeon(R) Gold 6230R CPU @ 2.10GHz
> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology cpuid tsc_known_freq pni pclmulqdq vmx ssse3 fma cx16 pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves arat umip pku ospke avx512_vnni md_clear arch_capabilities
>
> Online cpus: 0-3
> Offline cpus:
> BIOS frequency limitation: <Not Available>
> Frequency switch latency (ns): <Not Available>
> Available cpu frequencies: <Not Available>
> Current governor: <Not Available>
> Core performance/turbo boost: <Not Available>
>
> Memory: 4k page, physical 32654412k(274608k free), swap 975868k(0k free)
> Page Sizes: 4k
>
> vm_info: OpenJDK 64-Bit Server VM (17.0.7+7-LTS) for linux-amd64 JRE (17.0.7+7-LTS), built on May 16 2023 11:37:11 by "mockbuild" with gcc 8.5.0 20210514 (Red Hat 8.5.0-18)
>
> END.
> END OF LOG ERROR MESSAGE
>
> The tomcat JAVA_OPTs settings:
> JAVA_OPTS="$JAVA_OPTS -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -Doracle.jdbc.V8Compatible="true" -Djava.awt.headless=true -server -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xmx25g -Xms25g -XX:+HeapDumpOnOutOfMemoryError"
>
> ERDDAP status page:
> OS info: totalCPULoad=0.0068413615 processCPULoad=1.7713537E-4 totalMemory=31889MB freeMemory=1139MB totalSwapSpace=952MB freeSwapSpace=883MB Number of active requests=1 Number of threads: Tomcat-waiting=13, inotify=2, other=11 0 gc calls, 0 requests shed, and 0 dangerousMemoryEmails since last major LoadDatasets MemoryInUse= 78 MB (highWaterMark= 344 MB) (Xmx ~= 25600 MB)
>
> The VM hosting ERDDAP has 60 GB. I'm not sure where this "memory" issue is originating from. Can you help me please? The ERDDAP's two datasets are still accessible with no issues ( https://erddap.aoml.noaa.gov/gdp/erddap/status.html)
>
> Thank you in advance,
> Sam
>
> Thank you in advance,
> Sam
>
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