This question is related to Hadoop on Azure environment.
I am trying to use Runtime.exec() to execute a batch script in the reduce function. I could not get this running in Hadoop on Azure environment while it runs fine in the Hadoop on Linux. I tested the Runtime.exec() code snippet in my desktop (windows 7) environment and it runs fine there. I have made sure that I consume the output and error streams of the sub-process after Runtime.exec().
The batch script contains the below ( a single command):
c:\hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0024\attempt_201207121317_0024_r_000001_0\work\tool.exe
-f c:\hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0024\work\11_task_201207121317_0024_r_000001.out
-i c:\hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0024\attempt_201207121317_0024_r_000001_0\work\input.txt
I distribute the tool.exe and input.txt files using Distributed cache and it creates a symlink from the working directory. tool.exe and input.txt points to the actual files in the jobcache directory.
2012-07-16 04:31:51,613 INFO org.apache.hadoop.mapred.TaskRunner: Creating symlink: /hdfs/mapred/local/taskTracker/distcache/-978619214658189372_-1497645545_209290723/10.73.50.78tool.exe <- \hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0024\attempt_201207121317_0024_r_000001_0\work\tool.exe
2012-07-16 04:31:51,644 INFO org.apache.hadoop.mapred.TaskRunner: Creating symlink: /hdfs/mapred/local/taskTracker/distcache/-4944695173898834237_1545037473_2085004342/10.73.50.78input.txt <- \hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0024\attempt_201207121317_0024_r_000001_0\work\input.txt
The reducer gives the below error when it runs.
Command Execution Error: Cannot run program
"cmd /q /c c:\hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0024\work\11_task_201207121317_0024_r_0000011513543720767963399.bat":
CreateProcess error=2, The system cannot find the file specified
In another case, I tried running the same but without using the absolute paths.. The output stream from the sub-process is shown below:
c:\hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0022\attempt_201207121317_0022_r_000000_0\work>tool.exe -f /hdfs/mapred/local/taskTracker/nabeel/jobcache/job_201207121317_0022/work/1_task_201207121317_0022_r_000000.out
-i input.txt
I do not know how the job working directory paths and distributed cache works in Hadoop on Azure environment. Could you please let me know if I am missing something here (or) there is something I need to take care of while using Runtime.exec() in Hadoop on Azure environment.
Thanks,
.,._
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I am not familiar with Hadoop. But the error message seems to be obvious. It would be better if you can check whether the file exists.
c:\hdfs\mapred\local\taskTracker\nabeel\jobcache\job_201207121317_0024\work\11_task_201207121317_0024_r_0000011513543720767963399.bat
Best Regards,
Ming Xu
Related
I have a ReactJS-neo4j application, deployed on a cloud server. Currently, i create backups of my databases manually.
Now I want to automate this process. I want to automatically execute the above query every day
Can anyone tell me how to automate the above process ?
You need to change your neo4j configuration file found in <HOME_neo4j>/conf/neo4j.conf as below. The location of the file is different if you are not using Linux server, like Debian.
apoc.export.file.enabled=true
apoc.import.file.use_neo4j_config=false
The 2nd line will enable you to save the json file from default folder "import" to any folder you want.
Then open a terminal (or ssh) that connects to your cloud server. Go to <HOME_neo4j> directory where cypher-shell is installed. Copy and run this one liner script below.
echo "CALL apoc.export.json.all(\"/home/backups/deploymentName/backup_mydeployment.json\", { useTypes: true } )" | bin/cypher-shell -u neo4j -p <awesome_psw> --format plain
This will save the json file in /home/backups/deploymentName just like what you do in your neo4j browser.
I will leave it up to you on 1) how to add the timestamp YYMMDD0000_ in the filename via linux command and 2) schedule the job every midnight via crontab. Goodluck!
Ok, it is very strange. I have some init scripts that I would like to run when a cluster starts
cluster has the init script , which is in a file (in dbfs)
basically this
dbfs:/databricks/init-scripts/custom-cert.sh
Now , when I make the init script like this, it works (no ssl errors for my endpoints. Also, the event logs for the cluster shows the duration as 1 second for the init script
dbutils.fs.put("/databricks/init-scripts/custom-cert.sh", """#!/bin/bash
cp /dbfs/orgcertificates/orgcerts.crt /usr/local/share/ca-certificates/
sudo update-ca-certificates
echo "export REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt" >> /databricks/spark/conf/spark-env.sh
""")
However, if I just put the init script in an bash script and upload it to DBFS through a pipeline, the init script does not do anything. It executes , as per the event log but the execution duration is 0 sec.
I have the sh script in a file named
custom-cert.sh
with the same contents as above, i.e.
#!/bin/bash
cp /dbfs/orgcertificates/orgcerts.crt /usr/local/share/ca-certificates/
sudo update-ca-certificates
echo "export REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt"
but when I check /usr/local/share/ca-certificates/ , it does not contain /dbfs/orgcertificates/orgcerts.crt, even though the cluster init script has run.
Also, I have compared the contents of the init script in both cases and it least to the naked eye, I can't figure out any difference
i.e.
%sh
cat /dbfs/databricks/init-scripts/custom-cert.sh
shows the same contents in both the scenarios. What is the problem with the 2nd case?
EDIT: I read a bit more about init scripts and found that the logs of init scripts are written here
%sh
ls /databricks/init_scripts/
Looking at the err file in that location, it seems there is an error
sudo: update-ca-certificates
: command not found
Why is it that update-ca-certificates found in the first case but not when I put the same script in a sh script and upload it to dbfs (instead of executing the dbutils.fs.put within a notebook) ?
EDIT 2: In response to the first answer. After running the command
dbutils.fs.put("/databricks/init-scripts/custom-cert.sh", """#!/bin/bash
cp /dbfs/orgcertificates/orgcerts.crt /usr/local/share/ca-certificates/
sudo update-ca-certificates
echo "export REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt" >> /databricks/spark/conf/spark-env.sh
""")
the output is the file custom-cert.sh and then I restart the cluster with the init script location as dbfs:/databricks/init-scripts/custom-cert.sh and then it works. So, it is essentially the same content that the init script is reading (which is the generated sh script). Why can't it read it if I do not use dbfs put but just put the contents in bash file and upload it during the CI/CD process?
As we aware, An init script is a shell script that runs during startup of each cluster node before the Apache Spark driver or worker JVM start. case-2 When you run bash
command by using of %sh magic command means you are trying to execute this command in Local driver node. So that workers nodes is not able to access . But based on
case-1 , By using of %fs magic command you are trying run copy command (dbutils.fs.put )from root . So that along with driver node , other workers node also can access path .
Ref : https://docs.databricks.com/data/databricks-file-system.html#summary-table-and-diagram
It seems that my observations I made in the comments section of my question is the way to go.
I now create the init script using a databricks job that I run during the CI/CD pipeline from Azure DevOps.
The notebook has the commands
dbutils.fs.rm("/databricks/init-scripts/custom-cert.sh")
dbutils.fs.put("/databricks/init-scripts/custom-cert.sh", """#!/bin/bash
cp /dbfs/internal-certificates/certs.crt /usr/local/share/ca-certificates/
sudo update-ca-certificates
echo "export REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt" >> /databricks/spark/conf/spark-env.sh
""")
I then create a Databricks job (pointing to this notebook), the cluster is a job cluster which is just temporary . Of course , in my case , even this job creation is automated using a powershell script.
I then call this Databricks job in the release pipeline using again a Powershell script.
This creates the file
/databricks/init-scripts/custom-cert.sh
I then use this file in any other cluster that accesses my org's endpoints (without certificate errors).
I do not know (or still understand), why can't the same script file be just part of a repo and uploaded during the release process (instead of it being this Databricks job calling a notebook). I would love to know the reason . The other answer on this question does not hold true as you can see, that the cluster script is created by a job cluster and then accessed from another cluster as part of its init script.
It simply boils down to how the init script gets created.
But I get my job done. Just if it helps someone get their job done too.
I have raised a support case though to understand the reason.
I've been at it for days but could not solve my problem.
I am running:
mpiexec -hostfile ~/machines -nolocal -pernode mkdir -p $dstpath where $dstpath points to current directory and "machines" is a file containing:
node01
node02
node03
node04
This is the error output:
Failed to parse XML input with the minimalistic parser. If it was not
generated by hwloc, try enabling full XML support with libxml2.
[node01:06177] [[6421,0],0] ORTE_ERROR_LOG: Error in file base/plm_base_launch_support.c at line 891
--------------------------------------------------------------------------
ORTE was unable to reliably start one or more daemons.
This usually is caused by:
* not finding the required libraries and/or binaries on
one or more nodes. Please check your PATH and LD_LIBRARY_PATH
settings, or configure OMPI with --enable-orterun-prefix-by-default
* lack of authority to execute on one or more specified nodes.
Please verify your allocation and authorities.
* the inability to write startup files into /tmp (--tmpdir/orte_tmpdir_base).
Please check with your sys admin to determine the correct location to use.
* compilation of the orted with dynamic libraries when static are required
(e.g., on Cray). Please check your configure cmd line and consider using
one of the contrib/platform definitions for your system type.
* an inability to create a connection back to mpirun due to a
lack of common network interfaces and/or no route found between
them. Please check network connectivity (including firewalls
and network routing requirements).
--------------------------------------------------------------------------
[node01:06177] 1 more process has sent help message help-errmgr-base.txt / failed-daemon-launch
[node01:06177] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Failed to parse XML input with the minimalistic parser. If it was not
generated by hwloc, try enabling full XML support with libxml2.
[node01:06181] [[6417,0],0] ORTE_ERROR_LOG: Error in file base/plm_base_launch_support.c at line 891
I have 4 machines, node01 to node04. In order to log into these 4 nodes, I have to first log in to node00. I am trying to run some distributed graph functions. The graph software is installed in node01 and is supposed to be synchronised to the other nodes using mpiexec.
What I've done:
Made sure all passwordless login are setup, every machine can ssh to any other machine with no issues.
Have a hostfile in the home directory.
echo $PATH gives /home/myhome/bin:/home/myhome/.local/bin:/usr/include/openmpi:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
echo $LD_LIBRARY_PATH gives
/usr/lib/openmpi/lib
This has previously worked before, but it just suddenly started giving these errors. I got my administrator to install fresh machines but it still gave such errors. I've tried doing it one node at a time but it gave the same errors. I'm not entirely familiar with command line at all so please give me some suggestions. I've tried reinstalling OpenMPI from source and from sudo apt-get install openmpi-bin. I'm on Ubuntu 16.04 LTS.
You should focus on fixing:
Failed to parse XML input with the minimalistic parser. If it was not
generated by hwloc, try enabling full XML support with libxml2.
[node01:06177] [[6421,0],0] ORTE_ERROR_LOG: Error in file base/plm_base_launch_support.c at line 891
On a Unix server, I am running an application engine via the process scheduler.
In it, I am attempting to use a "zip" Unix command from within an "Exec" pplcode function.
However, I only get the error
PS_Exec(P): Error executing batch command with reason: No such file or directory (2)
I have tried it several ways. The most logical approach I thought was to change directory back to the root, then change to the specified directory so that I could easily use the zip command, such as the following...
Exec("cd / && cd /opt/psfin/pt850/dat/PSFIN1/PYMNT && zip INVREND INVREND.XML");
1643 12.20.34 0.000048 72: Exec("cd /opt/psfin/pt850/dat/PSFIN1/PYMNT");
1644 12.20.34 0.001343 PS_Exec(P): Error executing batch command with reason: No such file or directory (2)
I've even tried the following....just to see if anything works from within an Exec...
Exec("ls");
Sure enough, it gave the same error.
Now, some of you may be wondering, does the account that is associated with the process scheduler actually have authority on this particular directory path on the server ? Well, I was able to create the xml file given in the previous command with no problems.
I just cannot seem to be able to modify it with the Exec issuance of Unix commands.
I'm wondering if this is an error of rights and permissions from the unix server with regards to the operator id that the process scheduler is running from. However, given that it can create and write to a file there, I cannot understand why the Exec command would be met with any resistance....Just my gut shot in the dark...
Any help would be GREATLY appreciated!!!
Thanks,
Flynn
Not sure if you're still having an issue, but in your Exec code, adding the optional %FilePath_Absolute constant should help. When that constant is left off, PS automatically prefixes all commands with <PS_HOME>. You'll have to specify absolute paths with this flag on though. I've changed the command to something that should work.
Exec("zip /opt/psfin/pt850/dat/PSFIN1/PYMNT/INVREND /opt/psfin/pt850/dat/PSFIN1/PYMNT/INVREND.XML", %FilePath_Absolute);
The documentation at PeopleBooks is a little confusing sometimes, but it explains it fairly well in this case.
You can always store the absolute location in a variable and prefix that to your commands so you don't have to keep typing out /opt/psfin/pt850/dat/PSFIN1/PYMNT/.
i'm trying to run a simple executable using an Azure Web Role.
The executable is stored in the Web Role's local storage.
The executable produces a log.txt file once it has been run.
This is the method I am using to run the executable:
public void RunExecutable(string path)
{
Process.Start(path);
}
Where path is localStorage.RootPath + "Application.exe"
The problem I am facing is that when I open the local storage folder the executable is there however there is no log.txt file.
I have tested the executable, it works if I manually run it, it produces the log.txt file.
Can anyone see the problem?
Try setting an explicit WorkingDirectory for the process... I wonder if log.txt is being created, just not where you expect. (Or perhaps the app is trying to create log.txt but failing because of the permissions on the directory it's trying to create it in.)
If you remote desktop into the instance, can't you find the file created at E:\approot\ folder ? As Steve said, using a WorkingDirectory for the process will fix the issue
You can use Environment.GetEnvironmentVariable("RoleRoot") to construct the URL to your application root