From edd7bb86d2d44fa35423c4cc62dc821f46654583 Mon Sep 17 00:00:00 2001 From: aho Date: Mon, 2 Dec 2019 14:36:46 +0100 Subject: [PATCH 1/2] Revise --- inst/doc/faq.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index 3610bb2..9ab9769 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -314,20 +314,22 @@ This situation will occur if: 2. Launch jobs on an HPC where the connection with its login node is unidirectional (e.g., Power 9) Under this condition, the ecFlow UI will remain blue and will not update the status. -To solve this problem, run the following three lines in an R terminal after running Compute(): +To solve this problem, use `Collect()` in the R terminal after running Compute(): ```r res <- Compute(wf, ..., wait = FALSE) - saveRDS(res, file = 'test_data.Rds') - res <- readRDS('test_data.Rds') - result <- Collect(res, wait = TRUE) #it will update ecflow_ui status + result <- Collect(res, wait = TRUE) #it will update ecflow_ui status continuously, but will block the R session + result <- Collect(res, wait = FALSE) #it will return the ecflow_ui status once only, but will not block the R session ``` The last line will block the terminal but meanwhile update the status just like what you see with `wait = TRUE`. ### 3. Compute() successfully but then killed on R session -When Compute() on HPCs, the machines are able to process data which are much larger than the local workstation, so the computation works fine (i.e., on ec-Flow UI, the chunks show yellow in the end.) However, after the computation, the output will be sent back to local workstation. **If the returned data is larger than the available local memory space, your R session will be killed.** Therefore, always pre-check if the returned data will fit in your workstation free memory or not. If not, subset the input data or reduce the output size through more computation. +When Compute() on HPCs, the machines are able to process data which are much larger than the local workstation, so the computation works fine (i.e., on ec-Flow UI, the chunks show yellow in the end.) However, after the computation, the output will be sent back to local workstation. **If the returned data is larger than the available local memory space, your R session will be killed.** Therefore, always pre-check if the returned data will fit in your workstation free memory or not. If not, subset the input data or reduce the output size through more computation. + +Further explanation: though the complete output (i.e., merging all the chunks into one returned array) cannot be sent back to workstation, but the chunking results (.Rds file) are completed and saved in the directory '/STARTR_CHUNKING_'. If you still want to use the chunking results, you can find them there. + -- GitLab From 595f51fbae0e8c09e593491cdb54b6f6a63a8498 Mon Sep 17 00:00:00 2001 From: aho Date: Mon, 2 Dec 2019 15:14:04 +0100 Subject: [PATCH 2/2] Small revise --- inst/doc/faq.md | 1 - 1 file changed, 1 deletion(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index 9ab9769..b6df41c 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -325,7 +325,6 @@ To solve this problem, use `Collect()` in the R terminal after running Compute() result <- Collect(res, wait = FALSE) #it will return the ecflow_ui status once only, but will not block the R session ``` -The last line will block the terminal but meanwhile update the status just like what you see with `wait = TRUE`. ### 3. Compute() successfully but then killed on R session -- GitLab