Thanks for following up on this Ethan. As a side note, meanwhile SYSTEMML-635 has been resolved, so you don't necessarily need a SystemML-config file anymore.
Furthermore, this new issue is understandable too. SystemML uses a local tmp directory wherever we run our CP (singlenode in-memory) operations, e.g., for evictions if necessary. Normally, this is the driver process (on the node where you invoke SystemML) but also so-called remote parfor jobs, where we run our CP operations in each task and thus potentially any node of the cluster. Most likely you don't have permissions to create the specified directory there. Could you please try to use /tmp/systemml or any other directory where you have write access to workaround this? Regards, Matthias From: Ethan Xu <ethan.yifa...@gmail.com> To: dev@systemml.incubator.apache.org Date: 04/16/2016 04:13 PM Subject: Re: parfor fails Hi Matthias, Thank you very much for the explanation and a better solution. s = colSums (x==0) is more concise and works great! For experiment I tried the original parfor script with SystemML configuration file provided. On my cluster it's still failing with "PARFOR: Failed to execute loop in parallel". It looks like the failed MR jobs are caused by Caused by: org.apache.sysml.runtime.DMLRuntimeException: Failed to create non-existing local working directory:/path.to/ethan.xu/tmp/systemml That directory '/path.to/ethan.xu/tmp/systemml' exists on the local server, and it subdirectories named '_p22748_127.0.0.1' etc. It looks like other SystemML jobs had no trouble writing to it. The stderr and one failed MR log is attached. Thanks, Ethan On Thu, Apr 14, 2016 at 11:14 PM, Matthias Boehm <mbo...@us.ibm.com> wrote: just for completeness, this issue is tracked with https://issues.apache.org/jira/browse/SYSTEMML-635 and the fix will be available tomorrow. Regards, Matthias Matthias Boehm---04/14/2016 07:53:43 PM---Hi Ethan, thanks for catching this issue. The parfor script itself is perfectly fine From: Matthias Boehm/Almaden/IBM@IBMUS To: dev@systemml.incubator.apache.org Cc: "Ethan Xu" <ethan.yifa...@gmail.com> Date: 04/14/2016 07:53 PM Subject: Re: parfor fails Hi Ethan, thanks for catching this issue. The parfor script itself is perfectly fine but you encountered an interesting runtime bug. Usually, you can find the actual cause at the bottom of the stacktrace or in previous exceptions. I was able to reproduce this issue if NO systemml config file is provided (fails on parsing this non-existing config in the parfor mr job task setup). So the workaround is to put a SystemML-config.xml into the same directory. Interestingly, the issue did not show up in our testsuite because we always specify a default configuration there (which was until recently mandatory). As a side note, we strongly recommend parfor over for loops here because it runs the entire loop in 1 instead of 2396 MR jobs due to automatic data partitioning. However, for the specific example at hand, a data-parallel formulation (with "s = colSums(x==0)") would be even better as it allows for partial aggregation and hence reduces shuffle. Regards, Matthias Ethan Xu ---04/14/2016 01:34:24 PM---Hello, I have a quick question. The following script fails with this error: From: Ethan Xu <ethan.yifa...@gmail.com> To: dev@systemml.incubator.apache.org Date: 04/14/2016 01:34 PM Subject: parfor fails Hello, I have a quick question. The following script fails with this error: org.apache.sysml.runtime.DMLRuntimeException: PARFOR: Failed to execute loop in parallel. Here is the dml script: x=read($X); print("number of rows of x = " + nrow(x)); print("number of cols of x = " + ncol(x)); parfor(i in 1:ncol(x), check=0){ a = x[,i]; print("number of 0's in col " + i + " = " + sum(a == 0)); } where X is a 35 million by 2396 matrix (coded and dummy coded numerical matrix) on HDFS. The script runs fine with regular 'for' loops. Could someone explain why this script cannot run in parallel? Was it a wrong way to code parfor? Thanks, Ethan On Thu, Apr 14, 2016 at 11:14 PM, Matthias Boehm <mbo...@us.ibm.com> wrote: just for completeness, this issue is tracked with https://issues.apache.org/jira/browse/SYSTEMML-635 and the fix will be available tomorrow. Regards, Matthias Matthias Boehm---04/14/2016 07:53:43 PM---Hi Ethan, thanks for catching this issue. The parfor script itself is perfectly fine From: Matthias Boehm/Almaden/IBM@IBMUS To: dev@systemml.incubator.apache.org Cc: "Ethan Xu" <ethan.yifa...@gmail.com> Date: 04/14/2016 07:53 PM Subject: Re: parfor fails Hi Ethan, thanks for catching this issue. The parfor script itself is perfectly fine but you encountered an interesting runtime bug. Usually, you can find the actual cause at the bottom of the stacktrace or in previous exceptions. I was able to reproduce this issue if NO systemml config file is provided (fails on parsing this non-existing config in the parfor mr job task setup). So the workaround is to put a SystemML-config.xml into the same directory. Interestingly, the issue did not show up in our testsuite because we always specify a default configuration there (which was until recently mandatory). As a side note, we strongly recommend parfor over for loops here because it runs the entire loop in 1 instead of 2396 MR jobs due to automatic data partitioning. However, for the specific example at hand, a data-parallel formulation (with "s = colSums(x==0)") would be even better as it allows for partial aggregation and hence reduces shuffle. Regards, Matthias Ethan Xu ---04/14/2016 01:34:24 PM---Hello, I have a quick question. The following script fails with this error: From: Ethan Xu <ethan.yifa...@gmail.com> To: dev@systemml.incubator.apache.org Date: 04/14/2016 01:34 PM Subject: parfor fails Hello, I have a quick question. The following script fails with this error: org.apache.sysml.runtime.DMLRuntimeException: PARFOR: Failed to execute loop in parallel. Here is the dml script: x=read($X); print("number of rows of x = " + nrow(x)); print("number of cols of x = " + ncol(x)); parfor(i in 1:ncol(x), check=0){ a = x[,i]; print("number of 0's in col " + i + " = " + sum(a == 0)); } where X is a 35 million by 2396 matrix (coded and dummy coded numerical matrix) on HDFS. The script runs fine with regular 'for' loops. Could someone explain why this script cannot run in parallel? Was it a wrong way to code parfor? Thanks, Ethan [attachment "num-0-error-log2.txt" deleted by Matthias Boehm/Almaden/IBM] [attachment "reduce-log.txt" deleted by Matthias Boehm/Almaden/IBM]
