14495: Add dispatchcloud.EstimateScratchSpace()

Estimate size of Docker image based on collection size, and
incorporate that into disk space requirement.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/lib/dispatchcloud/node_size.go b/lib/dispatchcloud/node_size.go
index 1c36d6cf5bb770cb447b6f7f177d39c5ff7ef469..7706e411b4b721be1c1ff378ac49ebe03fc92333 100644 (file)
--- a/lib/dispatchcloud/node_size.go
+++ b/lib/dispatchcloud/node_size.go
@@ -8,7 +8,9 @@ import (
        "errors"
        "log"
        "os/exec"
+       "regexp"
        "sort"
+       "strconv"
        "strings"
        "time"
 
@@ -27,6 +29,65 @@ type ConstraintsNotSatisfiableError struct {
        AvailableTypes []arvados.InstanceType
 }
 
+var pdhRegexp = regexp.MustCompile(`^[0-9a-f]{32}\+(\d+)$`)
+
+// estimateDockerImageSize estimates how much disk space will be used
+// by a Docker image, given the PDH of a collection containing a
+// Docker image that was created by "arv-keepdocker".  Returns
+// estimated number of bytes of disk space that should be reserved.
+func estimateDockerImageSize(collectionPDH string) int64 {
+       m := pdhRegexp.FindStringSubmatch(collectionPDH)
+       if m == nil {
+               return 0
+       }
+       n, err := strconv.ParseInt(m[1], 10, 64)
+       if err != nil || n < 122 {
+               return 0
+       }
+       // To avoid having to fetch the collection, take advantage of
+       // the fact that the manifest storing a container image
+       // uploaded by arv-keepdocker has a predictable format, which
+       // allows us to estimate the size of the image based on just
+       // the size of the manifest.
+       //
+       // Use the following heuristic:
+       // - Start with the length of the mainfest (n)
+       // - Subtract 80 characters for the filename and file segment
+       // - Divide by 42 to get the number of block identifiers ('hash\+size\ ' is 32+1+8+1)
+       // - Assume each block is full, multiply by 64 MiB
+       return ((n - 80) / 42) * (64 * 1024 * 1024)
+}
+
+// EstimateScratchSpace estimates how much available disk space (in
+// bytes) is needed to run the container by summing the capacity
+// requested by 'tmp' mounts plus disk space required to load the
+// Docker image.
+func EstimateScratchSpace(ctr *arvados.Container) (needScratch int64) {
+       for _, m := range ctr.Mounts {
+               if m.Kind == "tmp" {
+                       needScratch += m.Capacity
+               }
+       }
+
+       // Account for disk space usage by Docker, assumes the following behavior:
+       // - Layer tarballs are buffered to disk during "docker load".
+       // - Individual layer tarballs are extracted from buffered
+       // copy to the filesystem
+       dockerImageSize := estimateDockerImageSize(ctr.ContainerImage)
+
+       // The buffer is only needed during image load, so make sure
+       // the baseline scratch space at least covers dockerImageSize,
+       // and assume it will be released to the job afterwards.
+       if needScratch < dockerImageSize {
+               needScratch = dockerImageSize
+       }
+
+       // Now reserve space for the extracted image on disk.
+       needScratch += dockerImageSize
+
+       return
+}
+
 // ChooseInstanceType returns the cheapest available
 // arvados.InstanceType big enough to run ctr.
 func ChooseInstanceType(cc *arvados.Cluster, ctr *arvados.Container) (best arvados.InstanceType, err error) {
@@ -35,12 +96,7 @@ func ChooseInstanceType(cc *arvados.Cluster, ctr *arvados.Container) (best arvad
                return
        }
 
-       needScratch := int64(0)
-       for _, m := range ctr.Mounts {
-               if m.Kind == "tmp" {
-                       needScratch += m.Capacity
-               }
-       }
+       needScratch := EstimateScratchSpace(ctr)
 
        needVCPUs := ctr.RuntimeConstraints.VCPUs
 

diff --git a/lib/dispatchcloud/node_size_test.go b/lib/dispatchcloud/node_size_test.go
index 91c6bb1049fb381d9070e747b1f076eec2f95dbc..e948538160ea943e3d4ea080c181e1e7cf108c48 100644 (file)
--- a/lib/dispatchcloud/node_size_test.go
+++ b/lib/dispatchcloud/node_size_test.go
@@ -119,3 +119,13 @@ func (*NodeSizeSuite) TestChoosePreemptable(c *check.C) {
        c.Check(best.Scratch >= 2*GiB, check.Equals, true)
        c.Check(best.Preemptible, check.Equals, true)
 }
+
+func (*NodeSizeSuite) TestScratchForDockerImage(c *check.C) {
+       n := EstimateScratchSpace(&arvados.Container{
+               ContainerImage: "d5025c0f29f6eef304a7358afa82a822+342",
+       })
+       // Actual image is 371.1 MiB (according to workbench)
+       // Estimated size is 384 MiB (402653184 bytes)
+       // Want to reserve 2x the estimated size, so 805306368 bytes
+       c.Check(n, check.Equals, int64(805306368))
+}

diff --git a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
index 084700d39bfad76b109078f29e81ecf82c40c5be..c4d535c999e0268385a18dfe7edcb00c5a9e5654 100644 (file)
--- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
+++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
@@ -229,12 +229,7 @@ func (disp *Dispatcher) checkSqueueForOrphans() {
 func (disp *Dispatcher) slurmConstraintArgs(container arvados.Container) []string {
        mem := int64(math.Ceil(float64(container.RuntimeConstraints.RAM+container.RuntimeConstraints.KeepCacheRAM+disp.ReserveExtraRAM) / float64(1048576)))
 
-       var disk int64
-       for _, m := range container.Mounts {
-               if m.Kind == "tmp" {
-                       disk += m.Capacity
-               }
-       }
+       disk := dispatchcloud.EstimateScratchSpace(&container)
        disk = int64(math.Ceil(float64(disk) / float64(1048576)))
        return []string{
                fmt.Sprintf("--mem=%d", mem),