votti
commented
4 years ago I am currently on holiday till July 22th, so I cannot test anything.
I think the issue is that the Zip is unzipped to a temporary directory, which likely is configured to be on the C and not on the data drive.
Thud I think setting the system temporary directory location to the data drive might work.
This can be done by setting the "TEMPDIR" environment variable zo a path on the data drive (eg “D:\") before calling the command. See here an example how to set environment variables from python: https://able.bio/rhett/how-to-set-and-get-environment-variables-in-python--274rgt5
Does this work?
On Thu, Jul 2, 2020, 23:18 aagamboa notifications@github.com wrote:
I am trying to run the pipeline with an .mcd file that is 19.7GB in size on Windows 10, version 1803. The processor is intel(R) Xenon(R) Silver 4112 CPU @2.60GHz 2.59. The operating type is a 64-bit operating system x64-based processor. the installed RAM is 48.0GB with 46.6GB usable. There is 1.17TB of free storage on the data drive.
when trying to execute the "convert zipped IMC acquisitions to input format" step I get the following error:
ERROR:root:Error in D:/cHL_PreProcessing/input/TMA_A1_1.zip Traceback (most recent call last): File "
", line 11, in File "C:\Users\GamboaA1\Documents\imctools\lib\site-packages\imctools\scripts\convertfolder2imcfolder.py", line 31, in convert_folder2imcfolder zipf.extractall(tmpdir.name) File "C:\Users\GamboaA1\Documents\imctools\lib\zipfile.py", line 1501, in extractall self._extract_member(zipinfo, path, pwd) File "C:\Users\GamboaA1\Documents\imctools\lib\zipfile.py", line 1556, in _extract_member shutil.copyfileobj(source, target) File "C:\Users\GamboaA1\Documents\imctools\lib\shutil.py", line 82, in copyfileobj fdst.write(buf) OSError: [Errno 28] No space left on device I have no issues running the provided example data set and also was able to run a smaller recently acquired mcd file (124.7 MB). 1TB of free space seems like it should be enough to handle the file, so I would like to know if you have any idea as to the memory RAM requirements for very large MCD files.
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aagamboa
I am trying to run the pipeline with an .mcd file that is 19.7GB in size on Windows 10, version 1803. The processor is intel(R) Xenon(R) Silver 4112 CPU @2.60GHz 2.59. The operating type is a 64-bit operating system x64-based processor. the installed RAM is 48.0GB with 46.6GB usable. There is 1.17TB of free storage on the data drive.
when trying to execute the "convert zipped IMC acquisitions to input format" step I get the following error:
ERROR:root:Error in D:/cHL_PreProcessing/input/TMA_A1_1.zip Traceback (most recent call last): File "<timed exec>", line 11, in <module> File "C:\Users\GamboaA1\Documents\imctools\lib\site-packages\imctools\scripts\convertfolder2imcfolder.py", line 31, in convert_folder2imcfolder zipf.extractall(tmpdir.name) File "C:\Users\GamboaA1\Documents\imctools\lib\zipfile.py", line 1501, in extractall self._extract_member(zipinfo, path, pwd) File "C:\Users\GamboaA1\Documents\imctools\lib\zipfile.py", line 1556, in _extract_member shutil.copyfileobj(source, target) File "C:\Users\GamboaA1\Documents\imctools\lib\shutil.py", line 82, in copyfileobj fdst.write(buf) OSError: [Errno 28] No space left on deviceI have no issues running the provided example data set and also was able to run a smaller recently acquired mcd file (124.7 MB).1TB of free space seems like it should be enough to handle the file, so I would like to know if you have any idea as to the memory RAM requirements for very large MCD files.