Huge CSV file with numeric and text data
5
I try to load a huge CSV file (~ 4 Gbyte), the data is both numeric and textual.
So, I can't load the data as a string.
str = OpenRead["train.csv"];
data = ReadList[str, String];
When I try to Import the file directly, my notebook is crash ( Win 10, WL 11.3, and my PC has 32G of RAM). The link to the data:
https://www.kaggle.com/c/microsoft-malware-prediction/data
To deal with this issue, I split the original file to a few parts and load each one and save in ".mx" format. Any suggestion on how to load the file in a more efficient way
list-manipulation performance-tuning data-acquisition
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
asked Dec 16 at 7:41
Kiril Danilchenko
798416
add a comment |
5
I try to load a huge CSV file (~ 4 Gbyte), the data is both numeric and textual.
So, I can't load the data as a string.
str = OpenRead["train.csv"];
data = ReadList[str, String];
When I try to Import the file directly, my notebook is crash ( Win 10, WL 11.3, and my PC has 32G of RAM). The link to the data:
https://www.kaggle.com/c/microsoft-malware-prediction/data
To deal with this issue, I split the original file to a few parts and load each one and save in ".mx" format. Any suggestion on how to load the file in a more efficient way
list-manipulation performance-tuning data-acquisition
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
asked Dec 16 at 7:41
Kiril Danilchenko
798416
Importis known to be somewhat memory inefficient. For simple text formats like CSV you could try to read in chunks. That will be especially efficient when you only need parts of the data (specific rows or columns). You will find several Q/A on this site which show examples how to do that...
– Albert Retey
Dec 16 at 20:20
Here are some links: mathematica.stackexchange.com/questions/65756/… mathematica.stackexchange.com/questions/35371/…
– FredrikD
Dec 17 at 7:27
add a comment |
5
5
5
1
I try to load a huge CSV file (~ 4 Gbyte), the data is both numeric and textual.
So, I can't load the data as a string.
str = OpenRead["train.csv"];
data = ReadList[str, String];
When I try to Import the file directly, my notebook is crash ( Win 10, WL 11.3, and my PC has 32G of RAM). The link to the data:
https://www.kaggle.com/c/microsoft-malware-prediction/data
To deal with this issue, I split the original file to a few parts and load each one and save in ".mx" format. Any suggestion on how to load the file in a more efficient way
list-manipulation performance-tuning data-acquisition
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
asked Dec 16 at 7:41
Kiril Danilchenko
798416
I try to load a huge CSV file (~ 4 Gbyte), the data is both numeric and textual.
So, I can't load the data as a string.
str = OpenRead["train.csv"];
data = ReadList[str, String];
When I try to Import the file directly, my notebook is crash ( Win 10, WL 11.3, and my PC has 32G of RAM). The link to the data:
https://www.kaggle.com/c/microsoft-malware-prediction/data
To deal with this issue, I split the original file to a few parts and load each one and save in ".mx" format. Any suggestion on how to load the file in a more efficient way
list-manipulation performance-tuning data-acquisition
list-manipulation performance-tuning data-acquisition
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
asked Dec 16 at 7:41
Kiril Danilchenko
798416
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
asked Dec 16 at 7:41
Kiril Danilchenko
798416
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
edited Dec 16 at 10:53
Αλέξανδρος Ζεγγ
4,0441928
4,0441928
asked Dec 16 at 7:41
Kiril Danilchenko
798416
asked Dec 16 at 7:41
Kiril Danilchenko
798416
asked Dec 16 at 7:41
Kiril Danilchenko
798416
798416
Importis known to be somewhat memory inefficient. For simple text formats like CSV you could try to read in chunks. That will be especially efficient when you only need parts of the data (specific rows or columns). You will find several Q/A on this site which show examples how to do that...
– Albert Retey
Dec 16 at 20:20
Here are some links: mathematica.stackexchange.com/questions/65756/… mathematica.stackexchange.com/questions/35371/…
– FredrikD
Dec 17 at 7:27
add a comment |
Importis known to be somewhat memory inefficient. For simple text formats like CSV you could try to read in chunks. That will be especially efficient when you only need parts of the data (specific rows or columns). You will find several Q/A on this site which show examples how to do that...
– Albert Retey
Dec 16 at 20:20
Here are some links: mathematica.stackexchange.com/questions/65756/… mathematica.stackexchange.com/questions/35371/…
– FredrikD
Dec 17 at 7:27
Import is known to be somewhat memory inefficient. For simple text formats like CSV you could try to read in chunks. That will be especially efficient when you only need parts of the data (specific rows or columns). You will find several Q/A on this site which show examples how to do that...– Albert Retey
Dec 16 at 20:20
Import is known to be somewhat memory inefficient. For simple text formats like CSV you could try to read in chunks. That will be especially efficient when you only need parts of the data (specific rows or columns). You will find several Q/A on this site which show examples how to do that...– Albert Retey
Dec 16 at 20:20
Here are some links: mathematica.stackexchange.com/questions/65756/… mathematica.stackexchange.com/questions/35371/…
– FredrikD
Dec 17 at 7:27
Here are some links: mathematica.stackexchange.com/questions/65756/… mathematica.stackexchange.com/questions/35371/…
– FredrikD
Dec 17 at 7:27
add a comment |
1 Answer
1
active
oldest
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7
I recognize this when larger files and/or depending on fileformats. A brute force solution is to increase the size for the java virtual machine, for example
`<< JLink`;InstallJava;
ReinstallJava[JVMArguments -> "-Xmx6144m"];`
answered Dec 16 at 9:20
FredrikD
9621822
Thank a lot, I will try this.
– Kiril Danilchenko
Dec 16 at 9:26
1
Since you have 32GB, you can of course increase the number after "-Xm"
– FredrikD
Dec 16 at 10:04
Have you actually tried that for CSV files? While there are several formats which are imported via java, I am not sure but think that importing CSV does not even use java, so changing the java stack size might not help in this case...
– Albert Retey
Dec 16 at 20:18
Good point. Is there any documentation on what Import uses for different formats? If import of CSV doesn't use Java then increasing the memory will not help. My own experience is that Import is a great function but a bit too "black boxy" and seems to be undergoing changes. E.g. I have programs that worked with 10.x that stopped working with 11.3 due to Unicode issues.
– FredrikD
Dec 17 at 7:25
add a comment |
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1 Answer
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7
I recognize this when larger files and/or depending on fileformats. A brute force solution is to increase the size for the java virtual machine, for example
`<< JLink`;InstallJava;
ReinstallJava[JVMArguments -> "-Xmx6144m"];`
answered Dec 16 at 9:20
FredrikD
9621822
Thank a lot, I will try this.
– Kiril Danilchenko
Dec 16 at 9:26
1
Since you have 32GB, you can of course increase the number after "-Xm"
– FredrikD
Dec 16 at 10:04
Have you actually tried that for CSV files? While there are several formats which are imported via java, I am not sure but think that importing CSV does not even use java, so changing the java stack size might not help in this case...
– Albert Retey
Dec 16 at 20:18
Good point. Is there any documentation on what Import uses for different formats? If import of CSV doesn't use Java then increasing the memory will not help. My own experience is that Import is a great function but a bit too "black boxy" and seems to be undergoing changes. E.g. I have programs that worked with 10.x that stopped working with 11.3 due to Unicode issues.
– FredrikD
Dec 17 at 7:25
add a comment |
7
I recognize this when larger files and/or depending on fileformats. A brute force solution is to increase the size for the java virtual machine, for example
`<< JLink`;InstallJava;
ReinstallJava[JVMArguments -> "-Xmx6144m"];`
answered Dec 16 at 9:20
FredrikD
9621822
Thank a lot, I will try this.
– Kiril Danilchenko
Dec 16 at 9:26
1
Since you have 32GB, you can of course increase the number after "-Xm"
– FredrikD
Dec 16 at 10:04
Have you actually tried that for CSV files? While there are several formats which are imported via java, I am not sure but think that importing CSV does not even use java, so changing the java stack size might not help in this case...
– Albert Retey
Dec 16 at 20:18
Good point. Is there any documentation on what Import uses for different formats? If import of CSV doesn't use Java then increasing the memory will not help. My own experience is that Import is a great function but a bit too "black boxy" and seems to be undergoing changes. E.g. I have programs that worked with 10.x that stopped working with 11.3 due to Unicode issues.
– FredrikD
Dec 17 at 7:25
add a comment |
7
7
7
I recognize this when larger files and/or depending on fileformats. A brute force solution is to increase the size for the java virtual machine, for example
`<< JLink`;InstallJava;
ReinstallJava[JVMArguments -> "-Xmx6144m"];`
answered Dec 16 at 9:20
FredrikD
9621822
I recognize this when larger files and/or depending on fileformats. A brute force solution is to increase the size for the java virtual machine, for example
`<< JLink`;InstallJava;
ReinstallJava[JVMArguments -> "-Xmx6144m"];`
answered Dec 16 at 9:20
FredrikD
9621822
answered Dec 16 at 9:20
FredrikD
9621822
answered Dec 16 at 9:20
FredrikD
9621822
answered Dec 16 at 9:20
FredrikD
9621822
9621822
Thank a lot, I will try this.
– Kiril Danilchenko
Dec 16 at 9:26
1
Since you have 32GB, you can of course increase the number after "-Xm"
– FredrikD
Dec 16 at 10:04
Have you actually tried that for CSV files? While there are several formats which are imported via java, I am not sure but think that importing CSV does not even use java, so changing the java stack size might not help in this case...
– Albert Retey
Dec 16 at 20:18
Good point. Is there any documentation on what Import uses for different formats? If import of CSV doesn't use Java then increasing the memory will not help. My own experience is that Import is a great function but a bit too "black boxy" and seems to be undergoing changes. E.g. I have programs that worked with 10.x that stopped working with 11.3 due to Unicode issues.
– FredrikD
Dec 17 at 7:25
add a comment |
Thank a lot, I will try this.
– Kiril Danilchenko
Dec 16 at 9:26
1
Since you have 32GB, you can of course increase the number after "-Xm"
– FredrikD
Dec 16 at 10:04
Have you actually tried that for CSV files? While there are several formats which are imported via java, I am not sure but think that importing CSV does not even use java, so changing the java stack size might not help in this case...
– Albert Retey
Dec 16 at 20:18
Good point. Is there any documentation on what Import uses for different formats? If import of CSV doesn't use Java then increasing the memory will not help. My own experience is that Import is a great function but a bit too "black boxy" and seems to be undergoing changes. E.g. I have programs that worked with 10.x that stopped working with 11.3 due to Unicode issues.
– FredrikD
Dec 17 at 7:25
Thank a lot, I will try this.
– Kiril Danilchenko
Dec 16 at 9:26
Thank a lot, I will try this.
– Kiril Danilchenko
Dec 16 at 9:26
1
1
Since you have 32GB, you can of course increase the number after "-Xm"
– FredrikD
Dec 16 at 10:04
Since you have 32GB, you can of course increase the number after "-Xm"
– FredrikD
Dec 16 at 10:04
Have you actually tried that for CSV files? While there are several formats which are imported via java, I am not sure but think that importing CSV does not even use java, so changing the java stack size might not help in this case...
– Albert Retey
Dec 16 at 20:18
Have you actually tried that for CSV files? While there are several formats which are imported via java, I am not sure but think that importing CSV does not even use java, so changing the java stack size might not help in this case...
– Albert Retey
Dec 16 at 20:18
Good point. Is there any documentation on what Import uses for different formats? If import of CSV doesn't use Java then increasing the memory will not help. My own experience is that Import is a great function but a bit too "black boxy" and seems to be undergoing changes. E.g. I have programs that worked with 10.x that stopped working with 11.3 due to Unicode issues.
– FredrikD
Dec 17 at 7:25
Good point. Is there any documentation on what Import uses for different formats? If import of CSV doesn't use Java then increasing the memory will not help. My own experience is that Import is a great function but a bit too "black boxy" and seems to be undergoing changes. E.g. I have programs that worked with 10.x that stopped working with 11.3 due to Unicode issues.
– FredrikD
Dec 17 at 7:25
add a comment |
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Importis known to be somewhat memory inefficient. For simple text formats like CSV you could try to read in chunks. That will be especially efficient when you only need parts of the data (specific rows or columns). You will find several Q/A on this site which show examples how to do that...– Albert Retey
Dec 16 at 20:20
Here are some links: mathematica.stackexchange.com/questions/65756/… mathematica.stackexchange.com/questions/35371/…
– FredrikD
Dec 17 at 7:27