Hello from Bioconductor, I'm developing a package to share R objects across clusters using boost library. The concept is similar to mmap package: https://cran.r-project.org/web/packages/mmap/index.html . However, I have a problem when I was trying to write Dataptr_method for the alternative string. Based on my understanding, the return value of the Dataptr_method function should be a vector of CHARSXP pointers. This design might be problematic in two ways: 1. The behavior of Dataptr_method function is inconsistent for string and the other ALTREP types. For the other types we return a vector of pure data in memory allocated outside of R, but for the string, we return a vector of R objects allocated by R. 2. It causes an unnecessary duplication of the data. In order to return CHARSXPs to R, It forces me to allocate CHARSXPs and copy the entire data to the R process. By contrast, for the other ALTREP types, say altreal, I can just return the pointer to R if the data is in the memory. The same problem occurs for Elt_method as well but is less serious since only one CHARSXPs is allocated. Because my package is designed for sharing a large R object. An allocation of the memory is undesired especially when the data is read-only in the code(eg. print function). I'm not sure if there are any solutions existed in the current R version, but I can imagine three workarounds: 1. Change the behavior of the R functions and use get_element function instead of Dataptr function. This would make the problem more memory-friendly but still cause the allocation. 2. Return a vector of const char* in Dataptr method. It would be very efficient and consistent with the return values of the other ALTREP types. 3. Provide an alternative CHARSXP. This might be the best solution since STRSXP behaves more like a list instead of a string, so an alternative CHARSXP fits the concept of ALTREP better. Since I'm not an expert in R so I might post a solved problem. I would be very happy and appreciate any suggestions regarding this problem. Best, Jiefei [[alternative HTML version deleted]]
Hi Jiefei, The issue here is that while the memory consequences of what you're describing may be true, this is simply how R handles character vector (what you're calling string) values internally. It doesn't actually have anything to do with ALTREP. Standard character vector SEXPs have an array of CHARSXP pointers in their payload (what is returned by DATAPTR) as well. As far as I know, this is important for string caching and is actually intended to save memory when the same string value appears many times in an R session (and takes up more bytes than a pointer), though I haven't dug around R's low-level string handling a ton. Either way though, this would be a much much larger change than just changing the ALTREP API (which for things like this explicitly and intentionally matches how the C api behaves for non-ALTREP SEXPs for compatability). Likewise the reason that get_element is going to return a CHARSXP, is because that is what STRING_ELT(x, i) returns (equivalent to (SEXP) DATAPTR(x)[i] ), so I don't think that can be changed either. One other thing to note, though, is that if your'e asking for the dataptr (and it isn't read only) then you're basically stepping out of ALTREP space anyway, so it makes sense that a normally laid-out STRSXP (with it's CHARSXP payload). Best, ~G On Thu, May 9, 2019 at 8:09 AM ??? <szwjf08 at gmail.com> wrote:> Hello from Bioconductor, > > I'm developing a package to share R objects across clusters using boost > library. The concept is similar to mmap package: > https://cran.r-project.org/web/packages/mmap/index.html . However, I have > a > problem when I was trying to write Dataptr_method for the alternative > string. > > Based on my understanding, the return value of the Dataptr_method function > should be a vector of CHARSXP pointers. This design might be problematic in > two ways: > > 1. The behavior of Dataptr_method function is inconsistent for string and > the other ALTREP types. For the other types we return a vector of pure data > in memory allocated outside of R, but for the string, we return a vector of > R objects allocated by R. > > 2. It causes an unnecessary duplication of the data. In order to return > CHARSXPs to R, It forces me to allocate CHARSXPs and copy the entire data > to the R process. By contrast, for the other ALTREP types, say altreal, I > can just return the pointer to R if the data is in the memory. > > The same problem occurs for Elt_method as well but is less serious since > only one CHARSXPs is allocated. Because my package is designed for sharing > a large R object. An allocation of the memory is undesired especially when > the data is read-only in the code(eg. print function). I'm not sure if > there are any solutions existed in the current R version, but I can imagine > three workarounds: > > 1. Change the behavior of the R functions and use get_element function > instead of Dataptr function. This would make the problem more > memory-friendly but still cause the allocation. > > 2. Return a vector of const char* in Dataptr method. It would be very > efficient and consistent with the return values of the other ALTREP types. > > 3. Provide an alternative CHARSXP. This might be the best solution since > STRSXP behaves more like a list instead of a string, so an alternative > CHARSXP fits the concept of ALTREP better. > > Since I'm not an expert in R so I might post a solved problem. I would be > very happy and appreciate any suggestions regarding this problem. > > Best, > Jiefei > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >[[alternative HTML version deleted]]
Hi Gabriel, Thanks for your explanation, I totally understand that it is almost impossible to change the data structure of STRSXP. However, what I'm proposing is not about changing the internal representation, but rather about how we design and use the ALTREP API. I might do not state the workarounds clearly as English is not my first language. Please let me explain them again in detail. 1. Update the existing R functions. When the ALTREP API Dataptr_or_null returns NULL, use get_element instead(or as best as we can). I have seen this pattern for some R functions, but somehow there are still some functions left that do not follow this rule. For example, print function will blindly call Dataptr (It even did not call Dataptr_or_null first) and forces me to allocate a large chunk of memory in R. Updating these functions would not completely solve the problem we are discussing but will make it less serious. 2. Update the ALTREP API, return a vector of const char *, and internally wrap them as CHARSXP. This can be a way to "hack" the R data structure with only a little cost to create the CHARSXP header. 3. Provide character ALTREP. Instead of using string ALTREP, we can define an alternative CHARSXP. By doing it we will completely solve the problem since the return value of the Dataptr of CHARSXP is a const char*. We do not have to change any internal representation of characters, it just requires a remap of the DATAPTR macro( or function?). Again, I sincerely appreciate your time and the detailed you provided. I'm looking forward to seeing any method to solve this problem in the current and future R release. Best, Jiefei Gabriel Becker <gabembecker at gmail.com> ?2019?5?9??? ??2:07???> Hi Jiefei, > > The issue here is that while the memory consequences of what you're > describing may be true, this is simply how R handles character vector (what > you're calling string) values internally. It doesn't actually have anything > to do with ALTREP. Standard character vector SEXPs have an array of CHARSXP > pointers in their payload (what is returned by DATAPTR) as well. > > As far as I know, this is important for string caching and is actually > intended to save memory when the same string value appears many times in an > R session (and takes up more bytes than a pointer), though I haven't dug > around R's low-level string handling a ton. Either way though, this would > be a much much larger change than just changing the ALTREP API (which for > things like this explicitly and intentionally matches how the C api behaves > for non-ALTREP SEXPs for compatability). > > Likewise the reason that get_element is going to return a CHARSXP, is > because that is what STRING_ELT(x, i) returns (equivalent to (SEXP) > DATAPTR(x)[i] ), so I don't think that can be changed either. > > One other thing to note, though, is that if your'e asking for the dataptr > (and it isn't read only) then you're basically stepping out of ALTREP space > anyway, so it makes sense that a normally laid-out STRSXP (with it's > CHARSXP payload). > > Best, > ~G > > On Thu, May 9, 2019 at 8:09 AM ??? <szwjf08 at gmail.com> wrote: > >> Hello from Bioconductor, >> >> I'm developing a package to share R objects across clusters using boost >> library. The concept is similar to mmap package: >> https://cran.r-project.org/web/packages/mmap/index.html . However, I >> have a >> problem when I was trying to write Dataptr_method for the alternative >> string. >> >> Based on my understanding, the return value of the Dataptr_method function >> should be a vector of CHARSXP pointers. This design might be problematic >> in >> two ways: >> >> 1. The behavior of Dataptr_method function is inconsistent for string and >> the other ALTREP types. For the other types we return a vector of pure >> data >> in memory allocated outside of R, but for the string, we return a vector >> of >> R objects allocated by R. >> >> 2. It causes an unnecessary duplication of the data. In order to return >> CHARSXPs to R, It forces me to allocate CHARSXPs and copy the entire data >> to the R process. By contrast, for the other ALTREP types, say altreal, I >> can just return the pointer to R if the data is in the memory. >> >> The same problem occurs for Elt_method as well but is less serious since >> only one CHARSXPs is allocated. Because my package is designed for sharing >> a large R object. An allocation of the memory is undesired especially when >> the data is read-only in the code(eg. print function). I'm not sure if >> there are any solutions existed in the current R version, but I can >> imagine >> three workarounds: >> >> 1. Change the behavior of the R functions and use get_element function >> instead of Dataptr function. This would make the problem more >> memory-friendly but still cause the allocation. >> >> 2. Return a vector of const char* in Dataptr method. It would be very >> efficient and consistent with the return values of the other ALTREP types. >> >> 3. Provide an alternative CHARSXP. This might be the best solution since >> STRSXP behaves more like a list instead of a string, so an alternative >> CHARSXP fits the concept of ALTREP better. >> >> Since I'm not an expert in R so I might post a solved problem. I would be >> very happy and appreciate any suggestions regarding this problem. >> >> Best, >> Jiefei >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >-- Jiefei Wang Room 2-501,Tangxuan,QilinGarden,NanshanDistrict,Shenzhen Guangdong,China Phone (+86)18312589584 szwjf8 at gmail.com [[alternative HTML version deleted]]